88 files changed, 1526 insertions, 574 deletions

diff --git a/bootstrap/package.yaml b/bootstrap/package.yaml
index ec5ecf2..26a7f74 100644
--- a/bootstrap/package.yaml
+++ b/bootstrap/package.yaml
@@ -58,3 +58,14 @@ tests:
     - -with-rtsopts=-N
     dependencies:
     - fpm
+  fpm-unittest:
+    main:                Trimmer.hs
+    source-dirs:         unit_test
+    ghc-options:
+    - -threaded
+    - -rtsopts
+    - -with-rtsopts=-N
+    dependencies:
+    - fpm
+    - hedge
+    - hedge-trimmer
diff --git a/bootstrap/src/Build.hs b/bootstrap/src/Build.hs
index cdcbb02..083e646 100644
--- a/bootstrap/src/Build.hs
+++ b/bootstrap/src/Build.hs
@@ -6,20 +6,19 @@ module Build
   )
 where
 
-import           Control.Applicative            ( (<|>) )
-import           Control.Monad                  ( filterM )
-import           Data.Char                      ( isAsciiLower
-                                                , isDigit
-                                                , toLower
+import           BuildModel                     ( CompileTimeInfo(..)
+                                                , RawSource(..)
+                                                , Source(..)
+                                                , constructCompileTimeInfo
+                                                , getAllObjectFiles
+                                                , getAvailableModules
+                                                , getSourceFileName
+                                                , processRawSource
                                                 )
 import           Data.List                      ( intercalate
                                                 , isSuffixOf
                                                 )
 import           Data.List.Utils                ( replace )
-import qualified Data.Map                      as Map
-import           Data.Maybe                     ( fromMaybe
-                                                , mapMaybe
-                                                )
 import           Development.Shake              ( FilePattern
                                                 , Change(ChangeModtimeAndDigest)
                                                 , cmd
@@ -36,39 +35,20 @@ import           Development.Shake              ( FilePattern
                                                 , shakeThreads
                                                 , want
                                                 , (<//>)
-                                                , (&%>)
                                                 , (%>)
-                                                , (?>)
+                                                , (&?>)
                                                 )
-import           Development.Shake.FilePath     ( dropExtension
-                                                , exe
-                                                , makeRelative
+import           Development.Shake.FilePath     ( exe
+                                                , splitDirectories
                                                 , (</>)
                                                 , (<.>)
-                                                , (-<.>)
                                                 )
+import           System.Environment             ( setEnv )
+import           System.Process                 ( system )
 import           System.Directory               ( createDirectoryIfMissing
                                                 , makeAbsolute
                                                 , withCurrentDirectory
                                                 )
-import           System.Environment             ( setEnv )
-import           System.FilePath                ( splitDirectories )
-import           System.Process                 ( system )
-import           Text.ParserCombinators.ReadP   ( ReadP
-                                                , char
-                                                , eof
-                                                , many
-                                                , many1
-                                                , option
-                                                , readP_to_S
-                                                , satisfy
-                                                , skipSpaces
-                                                , string
-                                                )
-
-type ModuleName = String
-
-data LineContents = ModuleUsed ModuleName | Other
 
 buildProgram
   :: FilePath
@@ -81,29 +61,23 @@ buildProgram
   -> FilePath
   -> [FilePath]
   -> IO ()
-buildProgram programDirectory libraryDirectories sourceExtensions buildDirectory compiler flags programName programSource archives
+buildProgram programDirectory' libraryDirectories sourceExtensions buildDirectory' compiler flags programName programSource archives
   = do
-    sourceFiles <- getDirectoriesFiles [programDirectory] sourceExtensions
-    canonicalProgramSource <- makeAbsolute $ programDirectory </> programSource
-    moduleSourceFiles <- filterM
-      (\source -> do
-        canonicalSource <- makeAbsolute source
-        return $ canonicalProgramSource /= canonicalSource
-      )
-      sourceFiles
-    let moduleObjectFiles = map
-          (sourceFileToObjectFile buildDirectory programDirectory)
-          moduleSourceFiles
-    let sourceFileLookupMap = createSourceFileLookupMap buildDirectory
-                                                        programDirectory
-                                                        moduleSourceFiles
-    let moduleLookupMap = createModuleLookupMap buildDirectory
-                                                programDirectory
-                                                moduleSourceFiles
-    otherModuleMaps <- mapM getLibraryModuleMap libraryDirectories
-    let allModuleMaps =
-          moduleLookupMap `Map.union` foldl Map.union Map.empty otherModuleMaps
+    let programDirectory = foldl1 (</>) (splitDirectories programDirectory')
+    let buildDirectory = foldl1 (</>) (splitDirectories buildDirectory')
     let includeFlags = map ("-I" ++) libraryDirectories
+    sourceFiles <- getDirectoriesFiles [programDirectory] sourceExtensions
+    rawSources  <- mapM sourceFileToRawSource sourceFiles
+    let sources' = map processRawSource rawSources
+    let isThisProgramOrNotProgram p@(Program{}) =
+          programSourceFileName p == programDirectory </> programSource
+        isThisProgramOrNotProgram _ = True
+    let sources          = filter isThisProgramOrNotProgram sources'
+    let availableModules = getAvailableModules sources
+    let compileTimeInfo = map
+          (\s -> constructCompileTimeInfo s availableModules buildDirectory)
+          sources
+    let objectFiles = getAllObjectFiles buildDirectory sources
     shake shakeOptions { shakeFiles    = buildDirectory
                        , shakeChange   = ChangeModtimeAndDigest
                        , shakeColor    = True
@@ -111,47 +85,28 @@ buildProgram programDirectory libraryDirectories sourceExtensions buildDirectory
                        , shakeProgress = progressSimple
                        }
       $ do
+          let infoToRule cti =
+                let obj                = compileTimeInfoObjectFileProduced cti
+                    other              = compileTimeInfoOtherFilesProduced cti
+                    directDependencies = compileTimeInfoDirectDependencies cti
+                    sourceFile         = compileTimeInfoSourceFileName cti
+                    fileMatcher f =
+                        let realf = foldl1 (</>) (splitDirectories f)
+                        in  if realf == obj || realf `elem` other
+                              then Just (obj : other)
+                              else Nothing
+                in  fileMatcher &?> \(objectFile : _) -> do
+                      need (sourceFile : directDependencies)
+                      cmd compiler
+                          ["-c", "-J" ++ buildDirectory]
+                          includeFlags
+                          flags
+                          ["-o", objectFile, sourceFile]
           want [buildDirectory </> programName <.> exe]
           buildDirectory </> programName <.> exe %> \executable -> do
-            let objectFile = sourceFileToObjectFile buildDirectory
-                                                    programDirectory
-                                                    programSource
-            let allObjectFiles = objectFile : moduleObjectFiles
-            need allObjectFiles
-            need archives
-            cmd compiler allObjectFiles archives ["-o", executable] flags
-          buildDirectory </> (map toLower programSource) -<.> "o" %> \objectFile -> do
-            let realObjectFile = foldl (</>) "" $ splitDirectories objectFile
-            let sourceFile     = programDirectory </> programSource
-            need [sourceFile]
-            modulesUsed <- liftIO $ getModulesUsed sourceFile
-            let moduleFilesNeeded =
-                  mapMaybe (`Map.lookup` allModuleMaps) modulesUsed
-            let includeFlags = map ("-I" ++) libraryDirectories
-            need moduleFilesNeeded
-            cmd compiler
-                ["-c", "-J" ++ buildDirectory]
-                includeFlags
-                flags
-                ["-o", objectFile, sourceFile]
-          map (\ext -> buildDirectory </> "*" <.> ext) ["o", "mod"]
-            &%> \[objectFile, moduleFile] -> do
-                  let realObjectFile =
-                        foldl (</>) "" $ splitDirectories objectFile
-                  let sourceFile = fromMaybe
-                        undefined
-                        (Map.lookup realObjectFile sourceFileLookupMap)
-                  need [sourceFile]
-                  modulesUsed <- liftIO $ getModulesUsed sourceFile
-                  let moduleFilesNeeded =
-                        mapMaybe (`Map.lookup` allModuleMaps) modulesUsed
-                  let includeFlags = map ("-I" ++) libraryDirectories
-                  need moduleFilesNeeded
-                  cmd compiler
-                      ["-c", "-J" ++ buildDirectory]
-                      includeFlags
-                      flags
-                      ["-o", objectFile, sourceFile]
+            need objectFiles
+            cmd compiler objectFiles archives ["-o", executable] flags
+          mapM_ infoToRule compileTimeInfo
 
 buildLibrary
   :: FilePath
@@ -164,14 +119,15 @@ buildLibrary
   -> IO (FilePath)
 buildLibrary libraryDirectory sourceExtensions buildDirectory compiler flags libraryName otherLibraryDirectories
   = do
+    let includeFlags = map ("-I" ++) otherLibraryDirectories
     sourceFiles <- getDirectoriesFiles [libraryDirectory] sourceExtensions
-    let sourceFileLookupMap =
-          createSourceFileLookupMap buildDirectory libraryDirectory sourceFiles
-    let moduleLookupMap =
-          createModuleLookupMap buildDirectory libraryDirectory sourceFiles
-    otherModuleMaps <- mapM getLibraryModuleMap otherLibraryDirectories
-    let allModuleMaps =
-          moduleLookupMap `Map.union` foldl Map.union Map.empty otherModuleMaps
+    rawSources  <- mapM sourceFileToRawSource sourceFiles
+    let sources          = map processRawSource rawSources
+    let availableModules = getAvailableModules sources
+    let compileTimeInfo = map
+          (\s -> constructCompileTimeInfo s availableModules buildDirectory)
+          sources
+    let objectFiles = getAllObjectFiles buildDirectory sources
     let archiveFile = buildDirectory </> "lib" ++ libraryName <.> "a"
     shake shakeOptions { shakeFiles    = buildDirectory
                        , shakeChange   = ChangeModtimeAndDigest
@@ -180,196 +136,30 @@ buildLibrary libraryDirectory sourceExtensions buildDirectory compiler flags lib
                        , shakeProgress = progressSimple
                        }
       $ do
-          map (\ext -> buildDirectory </> "*" <.> ext) ["o", "mod"]
-            &%> \[objectFile, moduleFile] -> do
-                  let realObjectFile =
-                        foldl (</>) "" $ splitDirectories objectFile
-                  let sourceFile = fromMaybe
-                        undefined
-                        (Map.lookup realObjectFile sourceFileLookupMap)
-                  need [sourceFile]
-                  modulesUsed <- liftIO $ getModulesUsed sourceFile
-                  let moduleFilesNeeded =
-                        mapMaybe (`Map.lookup` allModuleMaps) modulesUsed
-                  let includeFlags = map ("-I" ++) otherLibraryDirectories
-                  need moduleFilesNeeded
-                  cmd compiler
-                      ["-c", "-J" ++ buildDirectory]
-                      includeFlags
-                      flags
-                      ["-o", objectFile, sourceFile]
+          let infoToRule cti =
+                let obj                = compileTimeInfoObjectFileProduced cti
+                    other              = compileTimeInfoOtherFilesProduced cti
+                    directDependencies = compileTimeInfoDirectDependencies cti
+                    sourceFile         = compileTimeInfoSourceFileName cti
+                    fileMatcher f =
+                        let realf = foldl1 (</>) (splitDirectories f)
+                        in  if realf == obj || realf `elem` other
+                              then Just (obj : other)
+                              else Nothing
+                in  fileMatcher &?> \(objectFile : _) -> do
+                      need (sourceFile : directDependencies)
+                      cmd compiler
+                          ["-c", "-J" ++ buildDirectory]
+                          includeFlags
+                          flags
+                          ["-o", objectFile, sourceFile]
+          want [archiveFile]
           archiveFile %> \a -> do
-            let objectFiles = Map.keys sourceFileLookupMap
             need objectFiles
             cmd "ar" ["rs"] a objectFiles
-          want [archiveFile]
+          mapM_ infoToRule compileTimeInfo
     return archiveFile
 
--- A little wrapper around getDirectoryFiles so we can get files from multiple directories
-getDirectoriesFiles :: [FilePath] -> [FilePattern] -> IO [FilePath]
-getDirectoriesFiles dirs exts = getDirectoryFilesIO "" newPatterns
- where
-  newPatterns = concatMap appendExts dirs
-  appendExts dir = map ((dir <//> "*") ++) exts
-
-getLibraryModuleMap :: FilePath -> IO (Map.Map ModuleName FilePath)
-getLibraryModuleMap libraryDirectory = do
-  moduleFiles <- getDirectoriesFiles [libraryDirectory] ["*.mod"]
-  let moduleMap = foldl
-        Map.union
-        Map.empty
-        (map (\m -> Map.singleton (moduleFileToModuleName m) m) moduleFiles)
-  return moduleMap
- where
-  moduleFileToModuleName moduleFile =
-    map toLower $ dropExtension (makeRelative libraryDirectory moduleFile)
-
-createSourceFileLookupMap
-  :: FilePath -> FilePath -> [FilePath] -> Map.Map FilePath FilePath
-createSourceFileLookupMap buildDirectory libraryDirectory sourceFiles = foldl
-  Map.union
-  Map.empty
-  (map (createSourceToObjectMap buildDirectory libraryDirectory) sourceFiles)
-
-createModuleLookupMap
-  :: FilePath -> FilePath -> [FilePath] -> Map.Map ModuleName FilePath
-createModuleLookupMap buildDirectory libraryDirectory sourceFiles = foldl
-  Map.union
-  Map.empty
-  (map (createSourceToModuleMap buildDirectory libraryDirectory) sourceFiles)
-
-createSourceToModuleMap
-  :: FilePath -> FilePath -> FilePath -> Map.Map ModuleName FilePath
-createSourceToModuleMap buildDirectory libraryDirectory sourceFile =
-  Map.singleton
-    (sourceFileToModuleName libraryDirectory sourceFile)
-    (sourceFileToModFile buildDirectory libraryDirectory sourceFile)
-
-sourceFileToModuleName :: FilePath -> FilePath -> ModuleName
-sourceFileToModuleName libraryDirectory sourceFile =
-  map toLower $ pathSeparatorsToUnderscores
-    (dropExtension (makeRelative libraryDirectory sourceFile))
-
-createSourceToObjectMap
-  :: FilePath -> FilePath -> FilePath -> Map.Map FilePath FilePath
-createSourceToObjectMap buildDirectory libraryDirectory sourceFile =
-  Map.singleton
-    (sourceFileToObjectFile buildDirectory libraryDirectory sourceFile)
-    sourceFile
-
-sourceFileToObjectFile :: FilePath -> FilePath -> FilePath -> FilePath
-sourceFileToObjectFile buildDirectory libraryDirectory sourceFile =
-  (foldl (</>) "" $ splitDirectories buildDirectory)
-    </>  map
-           toLower
-           (pathSeparatorsToUnderscores
-             (makeRelative libraryDirectory sourceFile)
-           )
-    -<.> "o"
-
-sourceFileToExecutable :: FilePath -> FilePath -> FilePath -> FilePath
-sourceFileToExecutable buildDirectory appDirectory sourceFile =
-  buildDirectory
-    </>  pathSeparatorsToUnderscores (makeRelative appDirectory sourceFile)
-    -<.> exe
-
-sourceFileToModFile :: FilePath -> FilePath -> FilePath -> FilePath
-sourceFileToModFile buildDirectory libraryDirectory sourceFile =
-  buildDirectory
-    </>  map
-           toLower
-           (pathSeparatorsToUnderscores
-             (makeRelative libraryDirectory sourceFile)
-           )
-    -<.> "mod"
-
-pathSeparatorsToUnderscores :: FilePath -> FilePath
-pathSeparatorsToUnderscores fileName =
-  intercalate "_" (splitDirectories fileName)
-
-getModulesUsed :: FilePath -> IO [ModuleName]
-getModulesUsed sourceFile = do
-  fileLines <- readFileLinesIO sourceFile
-  let lineContents = map parseFortranLine fileLines
-  return $ contentsToModuleNames lineContents
-
-contentsToModuleNames :: [LineContents] -> [ModuleName]
-contentsToModuleNames = mapMaybe contentToMaybeModuleName
- where
-  contentToMaybeModuleName content = case content of
-    ModuleUsed moduleName -> Just moduleName
-    _                     -> Nothing
-
-readFileLinesIO :: FilePath -> IO [String]
-readFileLinesIO file = do
-  contents <- readFile file
-  return $ lines contents
-
-parseFortranLine :: String -> LineContents
-parseFortranLine line =
-  let line'  = map toLower line
-      result = readP_to_S doFortranLineParse line'
-  in  getResult result
- where
-  getResult (_ : (contents, _) : _) = contents
-  getResult [(contents, _)        ] = contents
-  getResult []                      = Other
-
-doFortranLineParse :: ReadP LineContents
-doFortranLineParse = option Other fortranUsefulContents
-
-fortranUsefulContents :: ReadP LineContents
-fortranUsefulContents = useStatement
-
-useStatement :: ReadP LineContents
-useStatement = do
-  skipSpaces
-  _ <- string "use"
-  skipAtLeastOneWhiteSpace
-  modName <- validIdentifier
-  skipSpaceCommaOrEnd
-  return $ ModuleUsed modName
-
-skipAtLeastOneWhiteSpace :: ReadP ()
-skipAtLeastOneWhiteSpace = do
-  _ <- many1 whiteSpace
-  return ()
-
-skipSpaceOrEnd :: ReadP ()
-skipSpaceOrEnd = eof <|> skipAtLeastOneWhiteSpace
-
-skipSpaceCommaOrEnd :: ReadP ()
-skipSpaceCommaOrEnd = eof <|> skipComma <|> skipAtLeastOneWhiteSpace
-
-skipComma :: ReadP ()
-skipComma = do
-  _ <- char ','
-  return ()
-
-whiteSpace :: ReadP Char
-whiteSpace = satisfy (`elem` " \t")
-
-validIdentifier :: ReadP String
-validIdentifier = do
-  first <- validFirstCharacter
-  rest  <- many validIdentifierCharacter
-  return $ first : rest
-
-validFirstCharacter :: ReadP Char
-validFirstCharacter = alphabet
-
-validIdentifierCharacter :: ReadP Char
-validIdentifierCharacter = alphabet <|> digit <|> underscore
-
-alphabet :: ReadP Char
-alphabet = satisfy isAsciiLower
-
-digit :: ReadP Char
-digit = satisfy isDigit
-
-underscore :: ReadP Char
-underscore = char '_'
-
 buildWithScript
   :: String
   -> FilePath
@@ -387,12 +177,11 @@ buildWithScript script projectDirectory buildDirectory compiler flags libraryNam
     setEnv "FC"     compiler
     setEnv "FFLAGS" (intercalate " " flags)
     setEnv "BUILD_DIR" $ unWindowsPath absoluteBuildDirectory
-    setEnv
-      "INCLUDE_DIRS"
-      (intercalate " " (map unWindowsPath absoluteLibraryDirectories))
+    setEnv "INCLUDE_DIRS"
+           (intercalate " " (map unWindowsPath absoluteLibraryDirectories))
     let archiveFile =
           (unWindowsPath absoluteBuildDirectory)
-            ++ "/lib"
+            ++  "/lib"
             ++  libraryName
             <.> "a"
     withCurrentDirectory
@@ -403,6 +192,18 @@ buildWithScript script projectDirectory buildDirectory compiler flags libraryNam
         | otherwise -> system (script ++ " " ++ archiveFile)
     return archiveFile
 
+-- A little wrapper around getDirectoryFiles so we can get files from multiple directories
+getDirectoriesFiles :: [FilePath] -> [FilePattern] -> IO [FilePath]
+getDirectoriesFiles dirs exts = getDirectoryFilesIO "" newPatterns
+ where
+  newPatterns = concatMap appendExts dirs
+  appendExts dir = map ((dir <//> "*") ++) exts
+
+sourceFileToRawSource :: FilePath -> IO RawSource
+sourceFileToRawSource sourceFile = do
+  contents <- readFile sourceFile
+  return $ RawSource sourceFile contents
+
 isMakefile :: String -> Bool
 isMakefile script | script == "Makefile"      = True
                   | script == "makefile"      = True
diff --git a/bootstrap/src/BuildModel.hs b/bootstrap/src/BuildModel.hs
new file mode 100644
index 0000000..95d3cac
--- /dev/null
+++ b/bootstrap/src/BuildModel.hs
@@ -0,0 +1,403 @@
+module BuildModel where
+
+import           Control.Applicative            ( (<|>) )
+import           Control.Monad                  ( when )
+import           Data.Char                      ( isAsciiLower
+                                                , isDigit
+                                                , toLower
+                                                )
+import           Data.Maybe                     ( fromMaybe
+                                                , mapMaybe
+                                                )
+import           Data.List                      ( intercalate )
+import           System.FilePath                ( (</>)
+                                                , (<.>)
+                                                , splitDirectories
+                                                )
+import           Text.ParserCombinators.ReadP   ( ReadP
+                                                , char
+                                                , eof
+                                                , many
+                                                , many1
+                                                , option
+                                                , readP_to_S
+                                                , satisfy
+                                                , skipSpaces
+                                                , string
+                                                )
+
+data LineContents =
+    ProgramDeclaration
+  | ModuleDeclaration String
+  | ModuleUsed String
+  | ModuleSubprogramDeclaration
+  | SubmoduleDeclaration String String String
+  | Other
+
+data RawSource = RawSource {
+    rawSourceFilename :: FilePath
+  , rawSourceContents :: String
+}
+
+data Source =
+  Program
+    { programSourceFileName :: FilePath
+    , programObjectFileName :: FilePath -> FilePath
+    , programModulesUsed :: [String]
+    }
+  | Module
+    { moduleSourceFileName :: FilePath
+    , moduleObjectFileName :: FilePath -> FilePath
+    , moduleModulesUsed :: [String]
+    , moduleName :: String
+    , moduleProducesSmod :: Bool
+    }
+  | Submodule
+    { submoduleSourceFileName :: FilePath
+    , submoduleObjectFileName :: FilePath -> FilePath
+    , submoduleModulesUsed :: [String]
+    , submoduleBaseModuleName :: String
+    , submoduleParentName :: String
+    , submoduleName :: String
+    }
+
+data CompileTimeInfo = CompileTimeInfo {
+    compileTimeInfoSourceFileName :: FilePath
+  , compileTimeInfoObjectFileProduced :: FilePath
+  , compileTimeInfoOtherFilesProduced :: [FilePath]
+  , compileTimeInfoDirectDependencies :: [FilePath]
+}
+
+processRawSource :: RawSource -> Source
+processRawSource rawSource =
+  let
+    sourceFileName = rawSourceFilename rawSource
+    parsedContents = parseContents rawSource
+    objectFileName =
+      \bd -> bd </> (pathSeparatorsToUnderscores sourceFileName) <.> "o"
+    modulesUsed = getModulesUsed parsedContents
+  in
+    if hasProgramDeclaration parsedContents
+      then Program { programSourceFileName = sourceFileName
+                   , programObjectFileName = objectFileName
+                   , programModulesUsed    = modulesUsed
+                   }
+      else if hasModuleDeclaration parsedContents
+        then Module
+          { moduleSourceFileName = sourceFileName
+          , moduleObjectFileName = objectFileName
+          , moduleModulesUsed    = modulesUsed
+          , moduleName           = getModuleName parsedContents
+          , moduleProducesSmod   = hasModuleSubprogramDeclaration parsedContents
+          }
+        else if hasSubmoduleDeclaration parsedContents
+          then Submodule
+            { submoduleSourceFileName = sourceFileName
+            , submoduleObjectFileName = objectFileName
+            , submoduleModulesUsed    = modulesUsed
+            , submoduleBaseModuleName = getSubmoduleBaseModuleName
+                                          parsedContents
+            , submoduleParentName     = getSubmoduleParentName parsedContents
+            , submoduleName           = getSubmoduleName parsedContents
+            }
+          else undefined
+
+getAvailableModules :: [Source] -> [String]
+getAvailableModules = mapMaybe maybeModuleName
+ where
+  maybeModuleName m@(Module{}) = Just $ moduleName m
+  maybeModuleName _            = Nothing
+
+getAllObjectFiles :: FilePath -> [Source] -> [FilePath]
+getAllObjectFiles buildDirectory sources = map getObjectFile sources
+ where
+  getObjectFile p@(Program{}  ) = (programObjectFileName p) buildDirectory
+  getObjectFile m@(Module{}   ) = (moduleObjectFileName m) buildDirectory
+  getObjectFile s@(Submodule{}) = (submoduleObjectFileName s) buildDirectory
+
+getSourceFileName :: Source -> FilePath
+getSourceFileName p@(Program{}  ) = programSourceFileName p
+getSourceFileName m@(Module{}   ) = moduleSourceFileName m
+getSourceFileName s@(Submodule{}) = submoduleSourceFileName s
+
+constructCompileTimeInfo :: Source -> [String] -> FilePath -> CompileTimeInfo
+constructCompileTimeInfo p@(Program{}) availableModules buildDirectory =
+  CompileTimeInfo
+    { compileTimeInfoSourceFileName     = programSourceFileName p
+    , compileTimeInfoObjectFileProduced = (programObjectFileName p)
+                                            buildDirectory
+    , compileTimeInfoOtherFilesProduced = []
+    , compileTimeInfoDirectDependencies = map
+      (\mName -> buildDirectory </> mName <.> "mod")
+      (filter (`elem` availableModules) (programModulesUsed p))
+    }
+constructCompileTimeInfo m@(Module{}) availableModules buildDirectory =
+  CompileTimeInfo
+    { compileTimeInfoSourceFileName     = moduleSourceFileName m
+    , compileTimeInfoObjectFileProduced = (moduleObjectFileName m)
+                                            buildDirectory
+    , compileTimeInfoOtherFilesProduced =
+      (buildDirectory </> moduleName m <.> "mod") : if moduleProducesSmod m
+        then [buildDirectory </> moduleName m <.> "smod"]
+        else []
+    , compileTimeInfoDirectDependencies = map
+      (\mName -> buildDirectory </> mName <.> "mod")
+      (filter (`elem` availableModules) (moduleModulesUsed m))
+    }
+constructCompileTimeInfo s@(Submodule{}) availableModules buildDirectory =
+  CompileTimeInfo
+    { compileTimeInfoSourceFileName     = submoduleSourceFileName s
+    , compileTimeInfoObjectFileProduced = (submoduleObjectFileName s)
+                                            buildDirectory
+    , compileTimeInfoOtherFilesProduced = [ buildDirectory
+                                            </> submoduleBaseModuleName s
+                                            ++  "@"
+                                            ++  submoduleName s
+                                            <.> "smod"
+                                          ]
+    , compileTimeInfoDirectDependencies =
+      (buildDirectory </> submoduleParentName s <.> "smod")
+        : (map (\mName -> buildDirectory </> mName <.> "mod")
+               (filter (`elem` availableModules) (submoduleModulesUsed s))
+          )
+    }
+
+pathSeparatorsToUnderscores :: FilePath -> FilePath
+pathSeparatorsToUnderscores fileName =
+  intercalate "_" (splitDirectories fileName)
+
+parseContents :: RawSource -> [LineContents]
+parseContents rawSource =
+  let fileLines = lines $ rawSourceContents rawSource
+  in  map parseFortranLine fileLines
+
+hasProgramDeclaration :: [LineContents] -> Bool
+hasProgramDeclaration parsedContents = case filter f parsedContents of
+  x : _ -> True
+  _     -> False
+ where
+  f lc = case lc of
+    ProgramDeclaration -> True
+    _                  -> False
+
+hasModuleDeclaration :: [LineContents] -> Bool
+hasModuleDeclaration parsedContents = case filter f parsedContents of
+  x : _ -> True
+  _     -> False
+ where
+  f lc = case lc of
+    ModuleDeclaration{} -> True
+    _                   -> False
+
+hasSubmoduleDeclaration :: [LineContents] -> Bool
+hasSubmoduleDeclaration parsedContents = case filter f parsedContents of
+  x : _ -> True
+  _     -> False
+ where
+  f lc = case lc of
+    SubmoduleDeclaration{} -> True
+    _                      -> False
+
+hasModuleSubprogramDeclaration :: [LineContents] -> Bool
+hasModuleSubprogramDeclaration parsedContents = case filter f parsedContents of
+  x : _ -> True
+  _     -> False
+ where
+  f lc = case lc of
+    ModuleSubprogramDeclaration -> True
+    _                           -> False
+
+getModulesUsed :: [LineContents] -> [String]
+getModulesUsed = mapMaybe contentToMaybeModuleName
+ where
+  contentToMaybeModuleName content = case content of
+    ModuleUsed moduleName -> Just moduleName
+    _                     -> Nothing
+
+getModuleName :: [LineContents] -> String
+getModuleName pc = head $ mapMaybe contentToMaybeModuleName pc
+ where
+  contentToMaybeModuleName content = case content of
+    ModuleDeclaration moduleName -> Just moduleName
+    _                            -> Nothing
+
+getSubmoduleBaseModuleName :: [LineContents] -> String
+getSubmoduleBaseModuleName pc = head $ mapMaybe contentToMaybeModuleName pc
+ where
+  contentToMaybeModuleName content = case content of
+    SubmoduleDeclaration baseModuleName submoduleParentName submoduleName ->
+      Just baseModuleName
+    _ -> Nothing
+
+getSubmoduleParentName :: [LineContents] -> String
+getSubmoduleParentName pc = head $ mapMaybe contentToMaybeModuleName pc
+ where
+  contentToMaybeModuleName content = case content of
+    SubmoduleDeclaration baseModuleName submoduleParentName submoduleName ->
+      Just submoduleParentName
+    _ -> Nothing
+
+getSubmoduleName :: [LineContents] -> String
+getSubmoduleName pc = head $ mapMaybe contentToMaybeModuleName pc
+ where
+  contentToMaybeModuleName content = case content of
+    SubmoduleDeclaration baseModuleName submoduleParentName submoduleName ->
+      Just submoduleName
+    _ -> Nothing
+
+readFileLinesIO :: FilePath -> IO [String]
+readFileLinesIO file = do
+  contents <- readFile file
+  return $ lines contents
+
+parseFortranLine :: String -> LineContents
+parseFortranLine line =
+  let line'  = map toLower line
+      result = readP_to_S doFortranLineParse line'
+  in  getResult result
+ where
+  getResult (_ : (contents, _) : _) = contents
+  getResult [(contents, _)        ] = contents
+  getResult []                      = Other
+
+doFortranLineParse :: ReadP LineContents
+doFortranLineParse = option Other fortranUsefulContents
+
+fortranUsefulContents :: ReadP LineContents
+fortranUsefulContents =
+  programDeclaration
+    <|> moduleSubprogramDeclaration
+    <|> moduleDeclaration
+    <|> submoduleDeclaration
+    <|> useStatement
+
+programDeclaration :: ReadP LineContents
+programDeclaration = do
+  skipSpaces
+  _ <- string "program"
+  skipAtLeastOneWhiteSpace
+  _ <- validIdentifier
+  return ProgramDeclaration
+
+moduleDeclaration :: ReadP LineContents
+moduleDeclaration = do
+  skipSpaces
+  _ <- string "module"
+  skipAtLeastOneWhiteSpace
+  moduleName <- validIdentifier
+  when (moduleName == "procedure") (fail "")
+  skipSpaceCommentOrEnd
+  return $ ModuleDeclaration moduleName
+
+submoduleDeclaration :: ReadP LineContents
+submoduleDeclaration = do
+  skipSpaces
+  _       <- string "submodule"
+  parents <- submoduleParents
+  let parentName = case parents of
+        (baseModule : []) -> baseModule
+        (multiple       ) -> (head multiple) ++ "@" ++ (last multiple)
+  skipSpaces
+  name <- validIdentifier
+  skipSpaceCommentOrEnd
+  return $ SubmoduleDeclaration (head parents) parentName name
+
+submoduleParents :: ReadP [String]
+submoduleParents = do
+  skipSpaces
+  _ <- char '('
+  skipSpaces
+  firstParent      <- validIdentifier
+  remainingParents <- many
+    (do
+      skipSpaces
+      _ <- char ':'
+      skipSpaces
+      name <- validIdentifier
+      return name
+    )
+  skipSpaces
+  _ <- char ')'
+  return $ firstParent : remainingParents
+
+useStatement :: ReadP LineContents
+useStatement = do
+  skipSpaces
+  _ <- string "use"
+  skipAtLeastOneWhiteSpace
+  modName <- validIdentifier
+  skipSpaceCommaOrEnd
+  return $ ModuleUsed modName
+
+moduleSubprogramDeclaration :: ReadP LineContents
+moduleSubprogramDeclaration = do
+  skipSpaces
+  skipProcedureQualifiers
+  _ <- string "module"
+  skipAtLeastOneWhiteSpace
+  _ <- string "function" <|> string "subroutine"
+  skipAtLeastOneWhiteSpace
+  return $ ModuleSubprogramDeclaration
+
+skipProcedureQualifiers :: ReadP ()
+skipProcedureQualifiers = do
+  many skipPossibleQualifier
+  return ()
+
+skipPossibleQualifier :: ReadP ()
+skipPossibleQualifier = do
+  _ <- string "pure" <|> string "elemental" <|> string "impure"
+  skipAtLeastOneWhiteSpace
+
+skipAtLeastOneWhiteSpace :: ReadP ()
+skipAtLeastOneWhiteSpace = do
+  _ <- many1 whiteSpace
+  return ()
+
+skipSpaceOrEnd :: ReadP ()
+skipSpaceOrEnd = eof <|> skipAtLeastOneWhiteSpace
+
+skipSpaceCommaOrEnd :: ReadP ()
+skipSpaceCommaOrEnd = eof <|> skipComma <|> skipAtLeastOneWhiteSpace
+
+skipSpaceCommentOrEnd :: ReadP ()
+skipSpaceCommentOrEnd = eof <|> skipComment <|> skipAtLeastOneWhiteSpace
+
+skipComma :: ReadP ()
+skipComma = do
+  _ <- char ','
+  return ()
+
+skipComment :: ReadP ()
+skipComment = do
+  _ <- char '!'
+  return ()
+
+skipAnything :: ReadP ()
+skipAnything = do
+  _ <- many (satisfy (const True))
+  return ()
+
+whiteSpace :: ReadP Char
+whiteSpace = satisfy (`elem` " \t")
+
+validIdentifier :: ReadP String
+validIdentifier = do
+  first <- validFirstCharacter
+  rest  <- many validIdentifierCharacter
+  return $ first : rest
+
+validFirstCharacter :: ReadP Char
+validFirstCharacter = alphabet
+
+validIdentifierCharacter :: ReadP Char
+validIdentifierCharacter = alphabet <|> digit <|> underscore
+
+alphabet :: ReadP Char
+alphabet = satisfy isAsciiLower
+
+digit :: ReadP Char
+digit = satisfy isDigit
+
+underscore :: ReadP Char
+underscore = char '_'
diff --git a/bootstrap/src/Fpm.hs b/bootstrap/src/Fpm.hs
index d9de668..115b63e 100644
--- a/bootstrap/src/Fpm.hs
+++ b/bootstrap/src/Fpm.hs
@@ -616,12 +616,15 @@ fetchDependency name version = do
         putStrLn "Simple dependencies are not yet supported :("
         undefined
       GitVersion versionSpec -> do
-        system
-          ("git init " ++ clonePath)
+        system ("git init " ++ clonePath)
         case gitVersionSpecRef versionSpec of
           Just ref -> do
             system
-              ("git -C " ++ clonePath ++ " fetch " ++ gitVersionSpecUrl versionSpec ++ " "
+              (  "git -C "
+              ++ clonePath
+              ++ " fetch "
+              ++ gitVersionSpecUrl versionSpec
+              ++ " "
               ++ (case ref of
                    Tag    tag    -> tag
                    Branch branch -> branch
@@ -630,9 +633,12 @@ fetchDependency name version = do
               )
           Nothing -> do
             system
-              ("git -C " ++ clonePath ++ " fetch " ++ gitVersionSpecUrl versionSpec)
-        system
-          ("git -C " ++ clonePath ++ " checkout -qf FETCH_HEAD")
+              (  "git -C "
+              ++ clonePath
+              ++ " fetch "
+              ++ gitVersionSpecUrl versionSpec
+              )
+        system ("git -C " ++ clonePath ++ " checkout -qf FETCH_HEAD")
         return (name, clonePath)
       PathVersion versionSpec -> return (name, pathVersionSpecPath versionSpec)
 
diff --git a/bootstrap/stack.yaml b/bootstrap/stack.yaml
index 68dcaaa..7147c40 100644
--- a/bootstrap/stack.yaml
+++ b/bootstrap/stack.yaml
@@ -42,6 +42,12 @@ packages:
 extra-deps:
 - git: https://github.com/kowainik/tomland.git
   commit: 536a5e6ffb148d0dd4e4c4b120913a6744097676
+- git: https://gitlab.com/everythingfunctional/hedge.git
+  commit: 1c6cba3b5f8e52cf317f2421aaca13a0ddab4e92
+  subdirs:
+    - .
+    - hedge-trimmer
+- quickcheck-with-counterexamples-1.2
 
 # Override default flag values for local packages and extra-deps
 # flags: {}
diff --git a/bootstrap/stack.yaml.lock b/bootstrap/stack.yaml.lock
index 15bfc22..0ca18ae 100644
--- a/bootstrap/stack.yaml.lock
+++ b/bootstrap/stack.yaml.lock
@@ -5,9 +5,6 @@
 
 packages:
 - completed:
-    cabal-file:
-      size: 6802
-      sha256: 85568a0280115b6e9a9f263cf4cfc72ad5a6eaeb2412875816adb82ea6a405bc
     name: tomland
     version: 1.3.0.0
     git: https://github.com/kowainik/tomland.git
@@ -18,6 +15,26 @@ packages:
   original:
     git: https://github.com/kowainik/tomland.git
     commit: 536a5e6ffb148d0dd4e4c4b120913a6744097676
+- completed:
+    subdir: hedge-trimmer
+    name: hedge-trimmer
+    version: 1.0.0.0
+    git: https://gitlab.com/everythingfunctional/hedge.git
+    pantry-tree:
+      size: 226
+      sha256: 19972f5b81c7627d6b66c852dfb7e0e67b3931ed4f418663c152717ce4ea267e
+    commit: 1c6cba3b5f8e52cf317f2421aaca13a0ddab4e92
+  original:
+    subdir: hedge-trimmer
+    git: https://gitlab.com/everythingfunctional/hedge.git
+    commit: 1c6cba3b5f8e52cf317f2421aaca13a0ddab4e92
+- completed:
+    hackage: quickcheck-with-counterexamples-1.2@sha256:d322d79008602df26f5eb4e1379e5b58bf1a92604df8601e71e200cfc3e847a3,1688
+    pantry-tree:
+      size: 724
+      sha256: 0046517e3cc2adebfce19d4aad05a06dcf55ec9e572fa1c661ba9abe81386484
+  original:
+    hackage: quickcheck-with-counterexamples-1.2
 snapshots:
 - completed:
     size: 524996
diff --git a/bootstrap/test b/bootstrap/test
deleted file mode 120000
index 419df4f..0000000
--- a/bootstrap/test
+++ /dev/null
@@ -1 +0,0 @@
-../test
\ No newline at end of file
diff --git a/test/Spec.hs b/bootstrap/test/Spec.hs
index 6fb4006..4e660e7 100644
--- a/test/Spec.hs
+++ b/bootstrap/test/Spec.hs
@@ -15,27 +15,53 @@ main = do
   testCircular
   testWithMakefile
   testMakefileComplex
+  testSubmodule
 
 testHelloWorld :: IO ()
 testHelloWorld =
-  withCurrentDirectory (example_path </> "hello_world") $ start $ Arguments (Run "") False ""
+  withCurrentDirectory (example_path </> "hello_world") $ start $ Arguments
+    (Run "")
+    False
+    ""
 
 testHelloComplex :: IO ()
 testHelloComplex =
-  withCurrentDirectory (example_path </> "hello_complex") $ start $ Arguments (Test "") False ""
+  withCurrentDirectory (example_path </> "hello_complex") $ start $ Arguments
+    (Test "")
+    False
+    ""
 
 testHelloFpm :: IO ()
 testHelloFpm =
-    withCurrentDirectory (example_path </> "hello_fpm") $ start $ Arguments (Run "") False ""
+  withCurrentDirectory (example_path </> "hello_fpm") $ start $ Arguments
+    (Run "")
+    False
+    ""
 
 testCircular :: IO ()
 testCircular =
-    withCurrentDirectory (example_path </> "circular_example") $ start $ Arguments (Test "") False ""
+  withCurrentDirectory (example_path </> "circular_example") $ start $ Arguments
+    (Test "")
+    False
+    ""
 
 testWithMakefile :: IO ()
 testWithMakefile =
-    withCurrentDirectory (example_path </> "with_makefile") $ start $ Arguments (Build) False ""
+  withCurrentDirectory (example_path </> "with_makefile") $ start $ Arguments
+    (Build)
+    False
+    ""
 
 testMakefileComplex :: IO ()
 testMakefileComplex =
-    withCurrentDirectory (example_path </> "makefile_complex") $ start $ Arguments (Run "") False ""
+  withCurrentDirectory (example_path </> "makefile_complex") $ start $ Arguments
+    (Run "")
+    False
+    ""
+
+testSubmodule :: IO ()
+testSubmodule =
+  withCurrentDirectory (example_path </> "submodules") $ start $ Arguments
+    (Build)
+    False
+    ""
diff --git a/bootstrap/test/example_packages b/bootstrap/test/example_packages
new file mode 120000
index 0000000..b7c12dc
--- /dev/null
+++ b/bootstrap/test/example_packages
@@ -0,0 +1 @@
+../../example_packages
\ No newline at end of file
diff --git a/bootstrap/unit_test/ModuleSourceConstructionTest.hs b/bootstrap/unit_test/ModuleSourceConstructionTest.hs
new file mode 100644
index 0000000..b98e9d3
--- /dev/null
+++ b/bootstrap/unit_test/ModuleSourceConstructionTest.hs
@@ -0,0 +1,83 @@
+module ModuleSourceConstructionTest
+  ( test
+  )
+where
+
+import           BuildModel                     ( RawSource(..)
+                                                , Source(..)
+                                                , processRawSource
+                                                )
+import           Hedge                          ( Result
+                                                , Test
+                                                , assertEquals
+                                                , assertThat
+                                                , fail'
+                                                , givenInput
+                                                , then'
+                                                , whenTransformed
+                                                )
+import           System.FilePath                ( (</>) )
+
+test :: IO (Test ())
+test = return $ givenInput
+  "a module"
+  exampleModule
+  [ whenTransformed
+      "processed to a source"
+      processRawSource
+      [ then' "it is a Module" checkIsModule
+      , then' "its source file name is the same as the original"
+              checkModuleSourceFileName
+      , then'
+        "its object file name is the 'flattened' path of the source file with '.o' appeneded"
+        checkModuleObjectFileName
+      , then' "it knows what modules it uses directly" checkModuleModulesUsed
+      , then' "it knows its name"                      checkModuleName
+      , then' "it can tell that it will produce a '.smod' file" checkSmod
+      ]
+  ]
+
+exampleModule :: RawSource
+exampleModule = RawSource moduleSourceFileName' $ unlines
+  [ "module some_module"
+  , "  use module1"
+  , "  USE MODULE2"
+  , "  implicit none"
+  , "  interface"
+  , "    pure module function some_func()"
+  , "      integer :: some_func"
+  , "    end function"
+  , "  end interface"
+  , "end module"
+  ]
+
+moduleSourceFileName' :: String
+moduleSourceFileName' = "some" </> "file" </> "somewhere.f90"
+
+checkIsModule :: Source -> Result
+checkIsModule Module{} = assertThat True
+checkIsModule _        = assertThat False
+
+checkModuleSourceFileName :: Source -> Result
+checkModuleSourceFileName m@(Module{}) =
+  assertEquals moduleSourceFileName' $ moduleSourceFileName m
+checkModuleSourceFileName _ = fail' "wasn't a Module"
+
+checkModuleObjectFileName :: Source -> Result
+checkModuleObjectFileName m@(Module{}) =
+  assertEquals ("." </> "some_file_somewhere.f90.o")
+    $ (moduleObjectFileName m) "."
+checkModuleObjectFileName _ = fail' "wasn't a Module"
+
+checkModuleModulesUsed :: Source -> Result
+checkModuleModulesUsed m@(Module{}) =
+  assertEquals ["module1", "module2"] $ moduleModulesUsed m
+checkModuleModulesUsed _ = fail' "wasn't a Module"
+
+checkModuleName :: Source -> Result
+checkModuleName m@(Module{}) = assertEquals "some_module" $ moduleName m
+checkModuleName _            = fail' "wasn't a Module"
+
+checkSmod :: Source -> Result
+checkSmod m@(Module{}) = assertThat $ moduleProducesSmod m
+checkSmod _ = fail' "wasn't a Module"
diff --git a/bootstrap/unit_test/ModuleToCompileInfoTest.hs b/bootstrap/unit_test/ModuleToCompileInfoTest.hs
new file mode 100644
index 0000000..5a1f0a8
--- /dev/null
+++ b/bootstrap/unit_test/ModuleToCompileInfoTest.hs
@@ -0,0 +1,70 @@
+module ModuleToCompileInfoTest
+  ( test
+  )
+where
+
+import           BuildModel                     ( CompileTimeInfo(..)
+                                                , Source(..)
+                                                , constructCompileTimeInfo
+                                                )
+import           Hedge                          ( Result
+                                                , Test
+                                                , assertEquals
+                                                , givenInput
+                                                , then'
+                                                , whenTransformed
+                                                )
+import           System.FilePath                ( (</>) )
+
+test :: IO (Test ())
+test = return $ givenInput
+  "a module and available modules"
+  (exampleModule, availableModules)
+  [ whenTransformed
+      "its compileTimeInfo is determined"
+      doCompileTimeTransformation
+      [ then' "it stil knows the original source file"     checkSourceFileName
+      , then' "it knows what object file will be produced" checkObjectFileName
+      , then' "the mod and smod files are also produced" checkOtherFilesProduced
+      , then' "the direct dependencies are only the available modules used"
+              checkDirectDependencies
+      ]
+  ]
+
+exampleModule :: Source
+exampleModule = Module
+  { moduleSourceFileName = moduleSourceFileName'
+  , moduleObjectFileName = \bd -> bd </> "some_file_somewhere.f90.o"
+  , moduleModulesUsed    = ["module1", "module2", "module3"]
+  , moduleName           = "some_module"
+  , moduleProducesSmod   = True
+  }
+
+moduleSourceFileName' :: FilePath
+moduleSourceFileName' = "some" </> "file" </> "somewhere.f90"
+
+availableModules :: [String]
+availableModules = ["module1", "module3"]
+
+doCompileTimeTransformation :: (Source, [String]) -> CompileTimeInfo
+doCompileTimeTransformation (programSource, otherSources) =
+  constructCompileTimeInfo programSource otherSources "build_dir"
+
+checkSourceFileName :: CompileTimeInfo -> Result
+checkSourceFileName cti =
+  assertEquals moduleSourceFileName' (compileTimeInfoSourceFileName cti)
+
+checkObjectFileName :: CompileTimeInfo -> Result
+checkObjectFileName cti = assertEquals
+  ("build_dir" </> "some_file_somewhere.f90.o")
+  (compileTimeInfoObjectFileProduced cti)
+
+checkOtherFilesProduced :: CompileTimeInfo -> Result
+checkOtherFilesProduced cti = assertEquals
+  ["build_dir" </> "some_module.mod", "build_dir" </> "some_module.smod"]
+  (compileTimeInfoOtherFilesProduced cti)
+
+checkDirectDependencies :: CompileTimeInfo -> Result
+checkDirectDependencies cti = assertEquals
+  ["build_dir" </> "module1.mod", "build_dir" </> "module3.mod"]
+  (compileTimeInfoDirectDependencies cti)
diff --git a/bootstrap/unit_test/ProgramSourceConstructionTest.hs b/bootstrap/unit_test/ProgramSourceConstructionTest.hs
new file mode 100644
index 0000000..6369965
--- /dev/null
+++ b/bootstrap/unit_test/ProgramSourceConstructionTest.hs
@@ -0,0 +1,69 @@
+module ProgramSourceConstructionTest
+  ( test
+  )
+where
+
+import           BuildModel                     ( RawSource(..)
+                                                , Source(..)
+                                                , processRawSource
+                                                )
+import           Hedge                          ( Result
+                                                , Test
+                                                , assertEquals
+                                                , assertThat
+                                                , fail'
+                                                , givenInput
+                                                , then'
+                                                , whenTransformed
+                                                )
+import           System.FilePath                ( (</>) )
+
+test :: IO (Test ())
+test = return $ givenInput
+  "a program"
+  exampleProgram
+  [ whenTransformed
+      "processed to a source"
+      processRawSource
+      [ then' "it is a Program" checkIsProgram
+      , then' "its source file name is the same as the original"
+              checkProgramSourceFileName
+      , then'
+        "its object file name is the 'flattened' path of the source file with '.o' appended"
+        checkProgramObjectFileName
+      , then' "it knows what modules it uses directly" checkProgramModulesUsed
+      ]
+  ]
+
+exampleProgram :: RawSource
+exampleProgram = RawSource programSourceFileName' $ unlines
+  [ "program some_program"
+  , "  use module1"
+  , "  USE MODULE2"
+  , "  implicit none"
+  , "  print *, \"Hello, World!\""
+  , "end program"
+  ]
+
+programSourceFileName' :: String
+programSourceFileName' = "some" </> "file" </> "somewhere.f90"
+
+checkIsProgram :: Source -> Result
+checkIsProgram Program{} = assertThat True
+checkIsProgram _         = assertThat False
+
+checkProgramSourceFileName :: Source -> Result
+checkProgramSourceFileName p@(Program{}) =
+  assertEquals programSourceFileName' $ programSourceFileName p
+checkProgramSourceFileName _ = fail' "wasn't a Program"
+
+checkProgramObjectFileName :: Source -> Result
+checkProgramObjectFileName p@(Program{}) =
+  assertEquals ("." </> "some_file_somewhere.f90.o")
+    $ (programObjectFileName p) "."
+checkProgramObjectFileName _ = fail' "wasn't a Program"
+
+checkProgramModulesUsed :: Source -> Result
+checkProgramModulesUsed p@(Program{}) =
+  assertEquals ["module1", "module2"] $ programModulesUsed p
+checkProgramModulesUsed _ = fail' "wasn't a Program"
diff --git a/bootstrap/unit_test/ProgramToCompileInfoTest.hs b/bootstrap/unit_test/ProgramToCompileInfoTest.hs
new file mode 100644
index 0000000..f17a3df
--- /dev/null
+++ b/bootstrap/unit_test/ProgramToCompileInfoTest.hs
@@ -0,0 +1,68 @@
+module ProgramToCompileInfoTest
+  ( test
+  )
+where
+
+import           BuildModel                     ( CompileTimeInfo(..)
+                                                , Source(..)
+                                                , constructCompileTimeInfo
+                                                )
+import           Hedge                          ( Result
+                                                , Test
+                                                , assertEmpty
+                                                , assertEquals
+                                                , givenInput
+                                                , then'
+                                                , whenTransformed
+                                                )
+import           System.FilePath                ( (</>) )
+
+test :: IO (Test ())
+test = return $ givenInput
+  "a program and available modules"
+  (exampleProgram, availableModules)
+  [ whenTransformed
+      "its compileTimeInfo is determined"
+      doCompileTimeTransformation
+      [ then' "it still knows the original source file"    checkSourceFileName
+      , then' "it knows what object file will be produced" checkObjectFileName
+      , then' "there are no other files produced" checkOtherFilesProduced
+      , then' "the direct dependencies are only the available modules used"
+              checkDirectDependencies
+      ]
+  ]
+
+exampleProgram :: Source
+exampleProgram = Program
+  { programSourceFileName = programSourceFileName'
+  , programObjectFileName = \bd -> bd </> "some_file_somewhere.f90.o"
+  , programModulesUsed    = ["module1", "module2", "module3"]
+  }
+
+programSourceFileName' :: FilePath
+programSourceFileName' = "some" </> "file" </> "somewhere.f90"
+
+availableModules :: [String]
+availableModules = ["module1", "module3"]
+
+doCompileTimeTransformation :: (Source, [String]) -> CompileTimeInfo
+doCompileTimeTransformation (programSource, otherSources) =
+  constructCompileTimeInfo programSource otherSources "build_dir"
+
+checkSourceFileName :: CompileTimeInfo -> Result
+checkSourceFileName cti =
+  assertEquals programSourceFileName' (compileTimeInfoSourceFileName cti)
+
+checkObjectFileName :: CompileTimeInfo -> Result
+checkObjectFileName cti = assertEquals
+  ("build_dir" </> "some_file_somewhere.f90.o")
+  (compileTimeInfoObjectFileProduced cti)
+
+checkOtherFilesProduced :: CompileTimeInfo -> Result
+checkOtherFilesProduced cti =
+  assertEmpty (compileTimeInfoOtherFilesProduced cti)
+
+checkDirectDependencies :: CompileTimeInfo -> Result
+checkDirectDependencies cti = assertEquals
+  ["build_dir" </> "module1.mod", "build_dir" </> "module3.mod"]
+  (compileTimeInfoDirectDependencies cti)
diff --git a/bootstrap/unit_test/SubmoduleSourceConstructionTest.hs b/bootstrap/unit_test/SubmoduleSourceConstructionTest.hs
new file mode 100644
index 0000000..d07a6ed
--- /dev/null
+++ b/bootstrap/unit_test/SubmoduleSourceConstructionTest.hs
@@ -0,0 +1,79 @@
+module SubmoduleSourceConstructionTest
+  ( test
+  )
+where
+
+import           BuildModel                     ( RawSource(..)
+                                                , Source(..)
+                                                , processRawSource
+                                                )
+import           Hedge                          ( Result
+                                                , Test
+                                                , assertEquals
+                                                , assertThat
+                                                , fail'
+                                                , givenInput
+                                                , then'
+                                                , whenTransformed
+                                                )
+import           System.FilePath                ( (</>) )
+
+test :: IO (Test ())
+test = return $ givenInput
+  "a submodule"
+  exampleSubmodule
+  [ whenTransformed
+      "processed to a source"
+      processRawSource
+      [ then' "it is a Submodule" checkIsSubmodule
+      , then' "its source file name is the same as the original"
+              checkSubmoduleSourceFileName
+      , then'
+        "its object file name is the 'flattened' path of the source file with '.o' appeneded"
+        checkSubmoduleObjectFileName
+      , then' "it knows what modules it uses directly" checkSubmoduleModulesUsed
+      , then' "it knows its parent's name"             checkSubmoduleParentName
+      , then' "it knows its name"                      checkSubmoduleName
+      ]
+  ]
+
+exampleSubmodule :: RawSource
+exampleSubmodule = RawSource submoduleSourceFileName' $ unlines
+  [ "submodule (some_module:parent) child"
+  , "  use module1"
+  , "  USE MODULE2"
+  , "  implicit none"
+  , "end submodule"
+  ]
+
+submoduleSourceFileName' :: String
+submoduleSourceFileName' = "some" </> "file" </> "somewhere.f90"
+
+checkIsSubmodule :: Source -> Result
+checkIsSubmodule Submodule{} = assertThat True
+checkIsSubmodule _           = assertThat False
+
+checkSubmoduleSourceFileName :: Source -> Result
+checkSubmoduleSourceFileName s@(Submodule{}) =
+  assertEquals submoduleSourceFileName' $ submoduleSourceFileName s
+checkSubmoduleSourceFileName _ = fail' "wasn't a Submodule"
+
+checkSubmoduleObjectFileName :: Source -> Result
+checkSubmoduleObjectFileName s@(Submodule{}) =
+  assertEquals ("." </> "some_file_somewhere.f90.o")
+    $ (submoduleObjectFileName s) "."
+checkSubmoduleObjectFileName _ = fail' "wasn't a Submodule"
+
+checkSubmoduleModulesUsed :: Source -> Result
+checkSubmoduleModulesUsed s@(Submodule{}) =
+  assertEquals ["module1", "module2"] $ submoduleModulesUsed s
+checkSubmoduleModulesUsed _ = fail' "wasn't a Submodule"
+
+checkSubmoduleParentName :: Source -> Result
+checkSubmoduleParentName s@(Submodule{}) =
+  assertEquals "some_module@parent" (submoduleParentName s)
+checkSubmoduleParentName _ = fail' "wasn't a Submodule"
+
+checkSubmoduleName :: Source -> Result
+checkSubmoduleName s@(Submodule{}) = assertEquals "child" $ submoduleName s
+checkSubmoduleName _               = fail' "wasn't a Submodule"
diff --git a/bootstrap/unit_test/SubmoduleToCompileInfoTest.hs b/bootstrap/unit_test/SubmoduleToCompileInfoTest.hs
new file mode 100644
index 0000000..d5d3ad8
--- /dev/null
+++ b/bootstrap/unit_test/SubmoduleToCompileInfoTest.hs
@@ -0,0 +1,75 @@
+module SubmoduleToCompileInfoTest
+  ( test
+  )
+where
+
+import           BuildModel                     ( CompileTimeInfo(..)
+                                                , Source(..)
+                                                , constructCompileTimeInfo
+                                                )
+import           Hedge                          ( Result
+                                                , Test
+                                                , assertEquals
+                                                , givenInput
+                                                , then'
+                                                , whenTransformed
+                                                )
+import           System.FilePath                ( (</>) )
+
+test :: IO (Test ())
+test = return $ givenInput
+  "a submodule and available modules"
+  (exampleSubmodule, availableModules)
+  [ whenTransformed
+      "its compileTimeInfo is determined"
+      doCompileTimeTransformation
+      [ then' "it still knows the original source file"    checkSourceFileName
+      , then' "it knows what object file will be produced" checkObjectFileName
+      , then' "the smod file is also produced" checkOtherFilesProduced
+      , then'
+        "the direct dependencies are the parent smod and the available modules used"
+        checkDirectDependencies
+      ]
+  ]
+
+exampleSubmodule :: Source
+exampleSubmodule = Submodule
+  { submoduleSourceFileName = submoduleSourceFileName'
+  , submoduleObjectFileName = \bd -> bd </> "some_file_somewhere.f90.o"
+  , submoduleModulesUsed    = ["module1", "module2", "module3"]
+  , submoduleBaseModuleName = "base_module"
+  , submoduleParentName     = "base_module@parent"
+  , submoduleName           = "some_submodule"
+  }
+
+submoduleSourceFileName' :: FilePath
+submoduleSourceFileName' = "some" </> "file" </> "somewhere.f90"
+
+availableModules :: [String]
+availableModules = ["module1", "module3"]
+
+doCompileTimeTransformation :: (Source, [String]) -> CompileTimeInfo
+doCompileTimeTransformation (programSource, otherSources) =
+  constructCompileTimeInfo programSource otherSources "build_dir"
+
+checkSourceFileName :: CompileTimeInfo -> Result
+checkSourceFileName cti =
+  assertEquals submoduleSourceFileName' (compileTimeInfoSourceFileName cti)
+
+checkObjectFileName :: CompileTimeInfo -> Result
+checkObjectFileName cti = assertEquals
+  ("build_dir" </> "some_file_somewhere.f90.o")
+  (compileTimeInfoObjectFileProduced cti)
+
+checkOtherFilesProduced :: CompileTimeInfo -> Result
+checkOtherFilesProduced cti = assertEquals
+  ["build_dir" </> "base_module@some_submodule.smod"]
+  (compileTimeInfoOtherFilesProduced cti)
+
+checkDirectDependencies :: CompileTimeInfo -> Result
+checkDirectDependencies cti = assertEquals
+  [ "build_dir" </> "base_module@parent.smod"
+  , "build_dir" </> "module1.mod"
+  , "build_dir" </> "module3.mod"
+  ]
+  (compileTimeInfoDirectDependencies cti)
diff --git a/bootstrap/unit_test/Trimmer.hs b/bootstrap/unit_test/Trimmer.hs
new file mode 100644
index 0000000..4e0f91d
--- /dev/null
+++ b/bootstrap/unit_test/Trimmer.hs
@@ -0,0 +1 @@
+{-# OPTIONS_GHC -F -pgmF hedge-trimmer #-}
diff --git a/ci/run_tests.bat b/ci/run_tests.bat
index 76e5349..7d0b178 100755
--- a/ci/run_tests.bat
+++ b/ci/run_tests.bat
@@ -15,20 +15,44 @@ if errorlevel 1 exit 1
 build\gfortran_debug\app\fpm
 if errorlevel 1 exit 1
 
-cd ..\test\example_packages\hello_world
+cd ..\example_packages\hello_world
 if errorlevel 1 exit 1
 
-..\..\..\fpm\build\gfortran_debug\app\fpm build
+..\..\fpm\build\gfortran_debug\app\fpm build
 if errorlevel 1 exit 1
 
 .\build\gfortran_debug\app\hello_world
 if errorlevel 1 exit 1
 
 
+cd ..\hello_fpm
+if errorlevel 1 exit 1
+
+..\..\fpm\build\gfortran_debug\app\fpm build
+if errorlevel 1 exit 1
+
+.\build\gfortran_debug\app\hello_fpm
+if errorlevel 1 exit 1
+
+
+cd ..\circular_test
+if errorlevel 1 exit 1
+
+..\..\fpm\build\gfortran_debug\app\fpm build
+if errorlevel 1 exit 1
+
+
+cd ..\circular_example
+if errorlevel 1 exit 1
+
+..\..\fpm\build\gfortran_debug\app\fpm build
+if errorlevel 1 exit 1
+
+
 cd ..\hello_complex
 if errorlevel 1 exit 1
 
-..\..\..\fpm\build\gfortran_debug\app\fpm build
+..\..\fpm\build\gfortran_debug\app\fpm build
 if errorlevel 1 exit 1
 
 .\build\gfortran_debug\app\say_Hello
@@ -47,7 +71,7 @@ if errorlevel 1 exit 1
 cd ..\hello_complex_2
 if errorlevel 1 exit 1
 
-..\..\..\fpm\build\gfortran_debug\app\fpm build
+..\..\fpm\build\gfortran_debug\app\fpm build
 if errorlevel 1 exit 1
 
 .\build\gfortran_debug\app\say_hello_world
@@ -65,7 +89,7 @@ if errorlevel 1 exit 1
 cd ..\auto_discovery_off
 if errorlevel 1 exit 1
 
-..\..\..\fpm\build\gfortran_debug\app\fpm build
+..\..\fpm\build\gfortran_debug\app\fpm build
 if errorlevel 1 exit 1
 
 .\build\gfortran_debug\app\auto_discovery_off
@@ -82,7 +106,7 @@ if exist .\build\gfortran_debug\test\unused_test exit /B 1
 cd ..\with_c
 if errorlevel 1 exit 1
 
-..\..\..\fpm\build\gfortran_debug\app\fpm build
+..\..\fpm\build\gfortran_debug\app\fpm build
 if errorlevel 1 exit 1
 
 .\build\gfortran_debug\app\with_c
@@ -92,15 +116,15 @@ if errorlevel 1 exit 1
 cd ..\submodules
 if errorlevel 1 exit 1
 
-..\..\..\fpm\build\gfortran_debug\app\fpm build
+..\..\fpm\build\gfortran_debug\app\fpm build
 if errorlevel 1 exit 1
 
 
 cd ..\program_with_module
 if errorlevel 1 exit 1
 
-..\..\..\fpm\build\gfortran_debug\app\fpm build
+..\..\fpm\build\gfortran_debug\app\fpm build
 if errorlevel 1 exit 1
 
 .\build\gfortran_debug\app\Program_with_module
-if errorlevel 1 exit 1
\ No newline at end of file
+if errorlevel 1 exit 1
diff --git a/ci/run_tests.sh b/ci/run_tests.sh
index adff2b3..a42653b 100755
--- a/ci/run_tests.sh
+++ b/ci/run_tests.sh
@@ -8,38 +8,48 @@ fpm run
 fpm test
 build/gfortran_debug/app/fpm
 
-cd ../test/example_packages/hello_world
-../../../fpm/build/gfortran_debug/app/fpm build
+cd ../example_packages/hello_world
+../../fpm/build/gfortran_debug/app/fpm build
 ./build/gfortran_debug/app/hello_world
 
+cd ../hello_fpm
+../../fpm/build/gfortran_debug/app/fpm build
+./build/gfortran_debug/app/hello_fpm
+
+cd ../circular_test
+../../fpm/build/gfortran_debug/app/fpm build
+
+cd ../circular_example
+../../fpm/build/gfortran_debug/app/fpm build
+
 cd ../hello_complex
-../../../fpm/build/gfortran_debug/app/fpm build
+../../fpm/build/gfortran_debug/app/fpm build
 ./build/gfortran_debug/app/say_Hello
 ./build/gfortran_debug/app/say_goodbye
 ./build/gfortran_debug/test/greet_test
 ./build/gfortran_debug/test/farewell_test
 
 cd ../hello_complex_2
-../../../fpm/build/gfortran_debug/app/fpm build
+../../fpm/build/gfortran_debug/app/fpm build
 ./build/gfortran_debug/app/say_hello_world
 ./build/gfortran_debug/app/say_goodbye
 ./build/gfortran_debug/test/greet_test
 ./build/gfortran_debug/test/farewell_test
 
 cd ../auto_discovery_off
-../../../fpm/build/gfortran_debug/app/fpm build
+../../fpm/build/gfortran_debug/app/fpm build
 ./build/gfortran_debug/app/auto_discovery_off
 ./build/gfortran_debug/test/my_test
 test ! -x ./build/gfortran_debug/app/unused
 test ! -x ./build/gfortran_debug/test/unused_test
 
 cd ../with_c
-../../../fpm/build/gfortran_debug/app/fpm build
+../../fpm/build/gfortran_debug/app/fpm build
 ./build/gfortran_debug/app/with_c
 
 cd ../submodules
-../../../fpm/build/gfortran_debug/app/fpm build
+../../fpm/build/gfortran_debug/app/fpm build
 
 cd ../program_with_module
-../../../fpm/build/gfortran_debug/app/fpm build
+../../fpm/build/gfortran_debug/app/fpm build
 ./build/gfortran_debug/app/Program_with_module
diff --git a/test/example_packages/README.md b/example_packages/README.md
index 79fadb1..65f4109 100644
--- a/test/example_packages/README.md
+++ b/example_packages/README.md
@@ -7,11 +7,11 @@ the features demonstrated in each package and which versions of fpm are supporte
 | Name                | Features                                                      | Bootstrap (Haskell) fpm | fpm |
 |---------------------|---------------------------------------------------------------|:-----------------------:|:---:|
 | auto_discovery_off  | Default layout with auto-discovery disabled                   |            N            |  Y  |
-| circular_example    | Local path dependency; circular dependency                    |            Y            |  N  |
-| circular_test       | Local path dependency; circular dependency                    |            Y            |  N  |
+| circular_example    | Local path dependency; circular dependency                    |            Y            |  Y  |
+| circular_test       | Local path dependency; circular dependency                    |            Y            |  Y  |
 | hello_complex       | Non-standard directory layout; multiple tests and executables |            Y            |  Y  |
 | hello_complex_2     | Auto-discovery of tests and executables with modules          |            N            |  Y  |
-| hello_fpm           | App-only; local path dependency                               |            Y            |  N  |
+| hello_fpm           | App-only; local path dependency                               |            Y            |  Y  |
 | hello_world         | App-only                                                      |            Y            |  Y  |
 | makefile_complex    | External build command (makefile); local path dependency      |            Y            |  N  |
 | program_with_module | App-only; module+program in single source file                |            Y            |  Y  |
diff --git a/test/example_packages/auto_discovery_off/app/main.f90 b/example_packages/auto_discovery_off/app/main.f90
index 8902dc6..8902dc6 100644
--- a/test/example_packages/auto_discovery_off/app/main.f90
+++ b/example_packages/auto_discovery_off/app/main.f90
diff --git a/test/example_packages/auto_discovery_off/app/unused.f90 b/example_packages/auto_discovery_off/app/unused.f90
index 57d8153..57d8153 100644
--- a/test/example_packages/auto_discovery_off/app/unused.f90
+++ b/example_packages/auto_discovery_off/app/unused.f90
diff --git a/test/example_packages/auto_discovery_off/fpm.toml b/example_packages/auto_discovery_off/fpm.toml
index 9a852df..9a852df 100644
--- a/test/example_packages/auto_discovery_off/fpm.toml
+++ b/example_packages/auto_discovery_off/fpm.toml
diff --git a/test/example_packages/auto_discovery_off/test/my_test.f90 b/example_packages/auto_discovery_off/test/my_test.f90
index fd59f9f..fd59f9f 100644
--- a/test/example_packages/auto_discovery_off/test/my_test.f90
+++ b/example_packages/auto_discovery_off/test/my_test.f90
diff --git a/test/example_packages/auto_discovery_off/test/unused_test.f90 b/example_packages/auto_discovery_off/test/unused_test.f90
index 5c42611..5c42611 100644
--- a/test/example_packages/auto_discovery_off/test/unused_test.f90
+++ b/example_packages/auto_discovery_off/test/unused_test.f90
diff --git a/test/example_packages/circular_example/.gitignore b/example_packages/circular_example/.gitignore
index a007fea..a007fea 100644
--- a/test/example_packages/circular_example/.gitignore
+++ b/example_packages/circular_example/.gitignore
diff --git a/test/example_packages/circular_example/fpm.toml b/example_packages/circular_example/fpm.toml
index c524ce5..c524ce5 100644
--- a/test/example_packages/circular_example/fpm.toml
+++ b/example_packages/circular_example/fpm.toml
diff --git a/test/example_packages/circular_example/src/greet_m.f90 b/example_packages/circular_example/src/greet_m.f90
index 2372f9a..2372f9a 100644
--- a/test/example_packages/circular_example/src/greet_m.f90
+++ b/example_packages/circular_example/src/greet_m.f90
diff --git a/test/example_packages/circular_example/test/main.f90 b/example_packages/circular_example/test/main.f90
index 5b7d803..5b7d803 100644
--- a/test/example_packages/circular_example/test/main.f90
+++ b/example_packages/circular_example/test/main.f90
diff --git a/test/example_packages/circular_test/.gitignore b/example_packages/circular_test/.gitignore
index a007fea..a007fea 100644
--- a/test/example_packages/circular_test/.gitignore
+++ b/example_packages/circular_test/.gitignore
diff --git a/test/example_packages/circular_test/fpm.toml b/example_packages/circular_test/fpm.toml
index 56cfa2e..56cfa2e 100644
--- a/test/example_packages/circular_test/fpm.toml
+++ b/example_packages/circular_test/fpm.toml
diff --git a/test/example_packages/circular_test/src/hello_test.f90 b/example_packages/circular_test/src/hello_test.f90
index 5a591c6..5a591c6 100644
--- a/test/example_packages/circular_test/src/hello_test.f90
+++ b/example_packages/circular_test/src/hello_test.f90
diff --git a/test/example_packages/hello_complex/.gitignore b/example_packages/hello_complex/.gitignore
index a007fea..a007fea 100644
--- a/test/example_packages/hello_complex/.gitignore
+++ b/example_packages/hello_complex/.gitignore
diff --git a/test/example_packages/hello_complex/apps/say_goodbye/say_goodbye.f90 b/example_packages/hello_complex/apps/say_goodbye/say_goodbye.f90
index 6966e79..6966e79 100644
--- a/test/example_packages/hello_complex/apps/say_goodbye/say_goodbye.f90
+++ b/example_packages/hello_complex/apps/say_goodbye/say_goodbye.f90
diff --git a/test/example_packages/hello_complex/apps/say_hello/say_Hello.f90 b/example_packages/hello_complex/apps/say_hello/say_Hello.f90
index cf4a742..cf4a742 100644
--- a/test/example_packages/hello_complex/apps/say_hello/say_Hello.f90
+++ b/example_packages/hello_complex/apps/say_hello/say_Hello.f90
diff --git a/test/example_packages/hello_complex/fpm.toml b/example_packages/hello_complex/fpm.toml
index 30ed293..30ed293 100644
--- a/test/example_packages/hello_complex/fpm.toml
+++ b/example_packages/hello_complex/fpm.toml
diff --git a/test/example_packages/hello_complex/source/farewell_m.f90 b/example_packages/hello_complex/source/farewell_m.f90
index fbc45ed..fbc45ed 100644
--- a/test/example_packages/hello_complex/source/farewell_m.f90
+++ b/example_packages/hello_complex/source/farewell_m.f90
diff --git a/test/example_packages/hello_complex/source/greet_m.f90 b/example_packages/hello_complex/source/greet_m.f90
index 38afd08..38afd08 100644
--- a/test/example_packages/hello_complex/source/greet_m.f90
+++ b/example_packages/hello_complex/source/greet_m.f90
diff --git a/test/example_packages/hello_complex/source/subdir/constants.f90 b/example_packages/hello_complex/source/subdir/constants.f90
index 59d6e5f..59d6e5f 100644
--- a/test/example_packages/hello_complex/source/subdir/constants.f90
+++ b/example_packages/hello_complex/source/subdir/constants.f90
diff --git a/test/example_packages/hello_complex/tests/farewell/farewell_test.f90 b/example_packages/hello_complex/tests/farewell/farewell_test.f90
index 0f21b18..0f21b18 100644
--- a/test/example_packages/hello_complex/tests/farewell/farewell_test.f90
+++ b/example_packages/hello_complex/tests/farewell/farewell_test.f90
diff --git a/test/example_packages/hello_complex/tests/greet/greet_test.f90 b/example_packages/hello_complex/tests/greet/greet_test.f90
index 41fa508..41fa508 100644
--- a/test/example_packages/hello_complex/tests/greet/greet_test.f90
+++ b/example_packages/hello_complex/tests/greet/greet_test.f90
diff --git a/test/example_packages/hello_complex_2/.gitignore b/example_packages/hello_complex_2/.gitignore
index a007fea..a007fea 100644
--- a/test/example_packages/hello_complex_2/.gitignore
+++ b/example_packages/hello_complex_2/.gitignore
diff --git a/test/example_packages/hello_complex_2/app/app_mod.f90 b/example_packages/hello_complex_2/app/app_mod.f90
index d69a228..d69a228 100644
--- a/test/example_packages/hello_complex_2/app/app_mod.f90
+++ b/example_packages/hello_complex_2/app/app_mod.f90
diff --git a/test/example_packages/hello_complex_2/app/say_goodbye.f90 b/example_packages/hello_complex_2/app/say_goodbye.f90
index db12cbf..db12cbf 100644
--- a/test/example_packages/hello_complex_2/app/say_goodbye.f90
+++ b/example_packages/hello_complex_2/app/say_goodbye.f90
diff --git a/test/example_packages/hello_complex_2/app/say_hello/app_hello_mod.f90 b/example_packages/hello_complex_2/app/say_hello/app_hello_mod.f90
index 5c426c8..c5795cb 100644
--- a/test/example_packages/hello_complex_2/app/say_hello/app_hello_mod.f90
+++ b/example_packages/hello_complex_2/app/say_hello/app_hello_mod.f90
@@ -1,4 +1,6 @@
 module app_hello_mod
 implicit none
 
+integer :: hello_int = 42
+
 end module app_hello_mod
diff --git a/test/example_packages/hello_complex_2/app/say_hello/say_Hello.f90 b/example_packages/hello_complex_2/app/say_hello/say_Hello.f90
index 3b69ba7..3b69ba7 100644
--- a/test/example_packages/hello_complex_2/app/say_hello/say_Hello.f90
+++ b/example_packages/hello_complex_2/app/say_hello/say_Hello.f90
diff --git a/test/example_packages/hello_complex_2/fpm.toml b/example_packages/hello_complex_2/fpm.toml
index 28c91d8..28c91d8 100644
--- a/test/example_packages/hello_complex_2/fpm.toml
+++ b/example_packages/hello_complex_2/fpm.toml
diff --git a/test/example_packages/hello_complex_2/src/farewell_m.f90 b/example_packages/hello_complex_2/src/farewell_m.f90
index 9fc75b9..9fc75b9 100644
--- a/test/example_packages/hello_complex_2/src/farewell_m.f90
+++ b/example_packages/hello_complex_2/src/farewell_m.f90
diff --git a/test/example_packages/hello_complex_2/src/greet_m.f90 b/example_packages/hello_complex_2/src/greet_m.f90
index 2372f9a..2372f9a 100644
--- a/test/example_packages/hello_complex_2/src/greet_m.f90
+++ b/example_packages/hello_complex_2/src/greet_m.f90
diff --git a/test/example_packages/hello_complex_2/test/farewell_test.f90 b/example_packages/hello_complex_2/test/farewell_test.f90
index dbe98d6..dbe98d6 100644
--- a/test/example_packages/hello_complex_2/test/farewell_test.f90
+++ b/example_packages/hello_complex_2/test/farewell_test.f90
diff --git a/test/example_packages/hello_complex_2/test/greet_test.f90 b/example_packages/hello_complex_2/test/greet_test.f90
index 38e9be0..38e9be0 100644
--- a/test/example_packages/hello_complex_2/test/greet_test.f90
+++ b/example_packages/hello_complex_2/test/greet_test.f90
diff --git a/test/example_packages/hello_complex_2/test/test_mod.f90 b/example_packages/hello_complex_2/test/test_mod.f90
index edb2626..edb2626 100644
--- a/test/example_packages/hello_complex_2/test/test_mod.f90
+++ b/example_packages/hello_complex_2/test/test_mod.f90
diff --git a/test/example_packages/hello_fpm/.gitignore b/example_packages/hello_fpm/.gitignore
index a007fea..a007fea 100644
--- a/test/example_packages/hello_fpm/.gitignore
+++ b/example_packages/hello_fpm/.gitignore
diff --git a/test/example_packages/hello_fpm/app/main.f90 b/example_packages/hello_fpm/app/main.f90
index 5df6d64..5df6d64 100644
--- a/test/example_packages/hello_fpm/app/main.f90
+++ b/example_packages/hello_fpm/app/main.f90
diff --git a/test/example_packages/hello_fpm/fpm.toml b/example_packages/hello_fpm/fpm.toml
index d94d904..d94d904 100644
--- a/test/example_packages/hello_fpm/fpm.toml
+++ b/example_packages/hello_fpm/fpm.toml
diff --git a/test/example_packages/hello_world/.gitignore b/example_packages/hello_world/.gitignore
index a007fea..a007fea 100644
--- a/test/example_packages/hello_world/.gitignore
+++ b/example_packages/hello_world/.gitignore
diff --git a/test/example_packages/hello_world/app/main.f90 b/example_packages/hello_world/app/main.f90
index d16022b..d16022b 100644
--- a/test/example_packages/hello_world/app/main.f90
+++ b/example_packages/hello_world/app/main.f90
diff --git a/test/example_packages/hello_world/fpm.toml b/example_packages/hello_world/fpm.toml
index b80e8d1..b80e8d1 100644
--- a/test/example_packages/hello_world/fpm.toml
+++ b/example_packages/hello_world/fpm.toml
diff --git a/test/example_packages/makefile_complex/.gitignore b/example_packages/makefile_complex/.gitignore
index a007fea..a007fea 100644
--- a/test/example_packages/makefile_complex/.gitignore
+++ b/example_packages/makefile_complex/.gitignore
diff --git a/test/example_packages/makefile_complex/Makefile b/example_packages/makefile_complex/Makefile
index 497c6b2..497c6b2 100644
--- a/test/example_packages/makefile_complex/Makefile
+++ b/example_packages/makefile_complex/Makefile
diff --git a/test/example_packages/makefile_complex/app/main.f90 b/example_packages/makefile_complex/app/main.f90
index ac9ed51..ac9ed51 100644
--- a/test/example_packages/makefile_complex/app/main.f90
+++ b/example_packages/makefile_complex/app/main.f90
diff --git a/test/example_packages/makefile_complex/fpm.toml b/example_packages/makefile_complex/fpm.toml
index 3282cbe..3282cbe 100644
--- a/test/example_packages/makefile_complex/fpm.toml
+++ b/example_packages/makefile_complex/fpm.toml
diff --git a/test/example_packages/makefile_complex/src/wrapper_mod.f90 b/example_packages/makefile_complex/src/wrapper_mod.f90
index e8028b5..e8028b5 100644
--- a/test/example_packages/makefile_complex/src/wrapper_mod.f90
+++ b/example_packages/makefile_complex/src/wrapper_mod.f90
diff --git a/test/example_packages/program_with_module/app/main.f90 b/example_packages/program_with_module/app/main.f90
index 59441f0..59441f0 100644
--- a/test/example_packages/program_with_module/app/main.f90
+++ b/example_packages/program_with_module/app/main.f90
diff --git a/test/example_packages/program_with_module/fpm.toml b/example_packages/program_with_module/fpm.toml
index bce6aa2..bce6aa2 100644
--- a/test/example_packages/program_with_module/fpm.toml
+++ b/example_packages/program_with_module/fpm.toml
diff --git a/test/example_packages/with_makefile/.gitignore b/example_packages/submodules/.gitignore
index a007fea..a007fea 100644
--- a/test/example_packages/with_makefile/.gitignore
+++ b/example_packages/submodules/.gitignore
diff --git a/test/example_packages/submodules/fpm.toml b/example_packages/submodules/fpm.toml
index cfc3d61..cfc3d61 100644
--- a/test/example_packages/submodules/fpm.toml
+++ b/example_packages/submodules/fpm.toml
diff --git a/test/example_packages/submodules/src/child1.f90 b/example_packages/submodules/src/child1.f90
index dbd0fa5..dbd0fa5 100644
--- a/test/example_packages/submodules/src/child1.f90
+++ b/example_packages/submodules/src/child1.f90
diff --git a/test/example_packages/submodules/src/child2.f90 b/example_packages/submodules/src/child2.f90
index 179cc32..179cc32 100644
--- a/test/example_packages/submodules/src/child2.f90
+++ b/example_packages/submodules/src/child2.f90
diff --git a/test/example_packages/submodules/src/grandchild.f90 b/example_packages/submodules/src/grandchild.f90
index 8c5aa17..8c5aa17 100644
--- a/test/example_packages/submodules/src/grandchild.f90
+++ b/example_packages/submodules/src/grandchild.f90
diff --git a/test/example_packages/submodules/src/parent.f90 b/example_packages/submodules/src/parent.f90
index 570827c..570827c 100644
--- a/test/example_packages/submodules/src/parent.f90
+++ b/example_packages/submodules/src/parent.f90
diff --git a/test/example_packages/with_c/app/main.f90 b/example_packages/with_c/app/main.f90
index 4d3174b..4d3174b 100644
--- a/test/example_packages/with_c/app/main.f90
+++ b/example_packages/with_c/app/main.f90
diff --git a/test/example_packages/with_c/fpm.toml b/example_packages/with_c/fpm.toml
index 97e3110..97e3110 100644
--- a/test/example_packages/with_c/fpm.toml
+++ b/example_packages/with_c/fpm.toml
diff --git a/test/example_packages/with_c/src/c_code.c b/example_packages/with_c/src/c_code.c
index 44604f0..44604f0 100644
--- a/test/example_packages/with_c/src/c_code.c
+++ b/example_packages/with_c/src/c_code.c
diff --git a/test/example_packages/with_c/src/with_c.f90 b/example_packages/with_c/src/with_c.f90
index edd839e..edd839e 100644
--- a/test/example_packages/with_c/src/with_c.f90
+++ b/example_packages/with_c/src/with_c.f90
diff --git a/example_packages/with_makefile/.gitignore b/example_packages/with_makefile/.gitignore
new file mode 100644
index 0000000..a007fea
--- /dev/null
+++ b/example_packages/with_makefile/.gitignore
@@ -0,0 +1 @@
+build/*
diff --git a/test/example_packages/with_makefile/Makefile b/example_packages/with_makefile/Makefile
index 51e72d4..51e72d4 100644
--- a/test/example_packages/with_makefile/Makefile
+++ b/example_packages/with_makefile/Makefile
diff --git a/test/example_packages/with_makefile/fpm.toml b/example_packages/with_makefile/fpm.toml
index 81dd02a..81dd02a 100644
--- a/test/example_packages/with_makefile/fpm.toml
+++ b/example_packages/with_makefile/fpm.toml
diff --git a/test/example_packages/with_makefile/src/hello_makefile.f90 b/example_packages/with_makefile/src/hello_makefile.f90
index 2d4d1a2..2d4d1a2 100644
--- a/test/example_packages/with_makefile/src/hello_makefile.f90
+++ b/example_packages/with_makefile/src/hello_makefile.f90
diff --git a/fpm/app/main.f90 b/fpm/app/main.f90
index be9b805..9982028 100644
--- a/fpm/app/main.f90
+++ b/fpm/app/main.f90
@@ -7,7 +7,8 @@ use fpm_command_line, only: &
         fpm_test_settings, &
         fpm_install_settings, &
         get_command_line_settings
-use fpm, only: cmd_build, cmd_install, cmd_new, cmd_run, cmd_test
+use fpm, only: cmd_build, cmd_install, cmd_run, cmd_test
+use fpm_cmd_new, only: cmd_new
 
 implicit none
 
diff --git a/fpm/src/fpm.f90 b/fpm/src/fpm.f90
index 4db35ba..36ee766 100644
--- a/fpm/src/fpm.f90
+++ b/fpm/src/fpm.f90
@@ -1,11 +1,10 @@
 module fpm
-
-use fpm_strings, only: string_t, str_ends_with
+use fpm_strings, only: string_t, str_ends_with, operator(.in.)
 use fpm_backend, only: build_package
 use fpm_command_line, only: fpm_build_settings, fpm_new_settings, &
                       fpm_run_settings, fpm_install_settings, fpm_test_settings
-use fpm_environment, only: run, get_os_type, OS_LINUX, OS_MACOS, OS_WINDOWS
-use fpm_filesystem, only: is_dir, join_path, number_of_rows, list_files, exists, basename, mkdir
+use fpm_environment, only: run
+use fpm_filesystem, only: is_dir, join_path, number_of_rows, list_files, exists, basename
 use fpm_model, only: srcfile_ptr, srcfile_t, fpm_model_t, &
                     FPM_SCOPE_UNKNOWN, FPM_SCOPE_LIB, &
                     FPM_SCOPE_DEP, FPM_SCOPE_APP, FPM_SCOPE_TEST
@@ -14,18 +13,134 @@ use fpm_sources, only: add_executable_sources, add_sources_from_dir, &
                        resolve_module_dependencies
 use fpm_manifest, only : get_package_data, default_executable, &
     default_library, package_t, default_test
-use fpm_error, only : error_t
+use fpm_error, only : error_t, fatal_error
 use fpm_manifest_test, only : test_t
 use,intrinsic :: iso_fortran_env, only : stdin=>input_unit,   &
                                        & stdout=>output_unit, &
                                        & stderr=>error_unit
+use fpm_manifest_dependency, only: dependency_t
 implicit none
 private
-public :: cmd_build, cmd_install, cmd_new, cmd_run, cmd_test
+public :: cmd_build, cmd_install, cmd_run, cmd_test
 
 contains
 
 
+recursive subroutine add_libsources_from_package(sources,package_list,package, &
+                                                  package_root,dev_depends,error)
+    ! Discover library sources in a package, recursively including dependencies
+    !
+    type(srcfile_t), allocatable, intent(inout), target :: sources(:)
+    type(string_t), allocatable, intent(inout) :: package_list(:)
+    type(package_t), intent(in) :: package
+    character(*), intent(in) :: package_root
+    logical, intent(in) :: dev_depends
+    type(error_t), allocatable, intent(out) :: error
+
+    ! Add package library sources
+    if (allocated(package%library)) then
+
+        call add_sources_from_dir(sources, join_path(package_root,package%library%source_dir), &
+                                    FPM_SCOPE_LIB, error=error)
+
+        if (allocated(error)) then
+            return
+        end if
+
+    end if
+
+    ! Add library sources from dependencies
+    if (allocated(package%dependency)) then
+
+        call add_dependencies(package%dependency)
+
+        if (allocated(error)) then
+            return
+        end if
+
+    end if
+
+    ! Add library sources from dev-dependencies
+    if (dev_depends .and. allocated(package%dev_dependency)) then
+
+        call add_dependencies(package%dev_dependency)
+
+        if (allocated(error)) then
+            return
+        end if
+
+    end if
+
+    contains
+
+    subroutine add_dependencies(dependency_list)
+        type(dependency_t), intent(in) :: dependency_list(:)
+
+        integer :: i
+        type(string_t) :: dep_name
+        type(package_t) :: dependency
+
+        character(:), allocatable :: dependency_path
+
+        do i=1,size(dependency_list)
+            
+            if (dependency_list(i)%name .in. package_list) then
+                cycle
+            end if
+
+            if (allocated(dependency_list(i)%git)) then
+
+                dependency_path = join_path('build','dependencies',dependency_list(i)%name)
+
+                if (.not.exists(join_path(dependency_path,'fpm.toml'))) then
+                    call dependency_list(i)%git%checkout(dependency_path, error)
+                    if (allocated(error)) return
+                end if
+
+            else if (allocated(dependency_list(i)%path)) then
+                
+                dependency_path = join_path(package_root,dependency_list(i)%path)
+
+            end if
+
+            call get_package_data(dependency, &
+                    join_path(dependency_path,"fpm.toml"), error)
+
+            if (allocated(error)) then
+                error%message = 'Error while parsing manifest for dependency package at:'//&
+                                new_line('a')//join_path(dependency_path,"fpm.toml")//&
+                                new_line('a')//error%message
+                return
+            end if
+
+            if (.not.allocated(dependency%library) .and. &
+                    exists(join_path(dependency_path,"src"))) then
+                allocate(dependency%library)
+                dependency%library%source_dir = "src"
+            end if
+
+            
+            call add_libsources_from_package(sources,package_list,dependency, &
+                package_root=dependency_path, &
+                dev_depends=.false., error=error)
+            
+            if (allocated(error)) then
+                error%message = 'Error while processing sources for dependency package "'//&
+                                new_line('a')//dependency%name//'"'//&
+                                new_line('a')//error%message
+                return
+            end if
+
+            dep_name%s = dependency_list(i)%name
+            package_list = [package_list, dep_name]
+
+        end do
+
+    end subroutine add_dependencies
+
+end subroutine add_libsources_from_package
+
+
 subroutine build_model(model, settings, package, error)
     ! Constructs a valid fpm model from command line settings and toml manifest
     !
@@ -35,8 +150,13 @@ subroutine build_model(model, settings, package, error)
     type(error_t), allocatable, intent(out) :: error
     integer :: i
 
+    type(string_t), allocatable :: package_list(:)
+
     model%package_name = package%name
 
+    allocate(package_list(1))
+    package_list(1)%s = package%name
+
     ! #TODO: Choose flags and output directory based on cli settings & manifest inputs
     model%fortran_compiler = 'gfortran'
 
@@ -98,17 +218,13 @@ subroutine build_model(model, settings, package, error)
 
     endif
 
-    if (allocated(package%library)) then
-
-        call add_sources_from_dir(model%sources, package%library%source_dir, &
-                                    FPM_SCOPE_LIB, error=error)
-
-        if (allocated(error)) then
-            return
-        endif
-
+    ! Add library sources, including local dependencies
+    call add_libsources_from_package(model%sources,package_list,package, &
+                                      package_root='.',dev_depends=.true.,error=error)
+    if (allocated(error)) then
+        return
+    end if
 
-    endif
     if(settings%list)then
         do i=1,size(model%sources)
             write(stderr,'(*(g0,1x))')'fpm::build<INFO>:file expected at',model%sources(i)%file_name, &
@@ -168,160 +284,6 @@ type(fpm_install_settings), intent(in) :: settings
     error stop 8
 end subroutine cmd_install
 
-
-subroutine cmd_new(settings) ! --with-executable F --with-test F '
-type(fpm_new_settings), intent(in) :: settings
-integer :: ierr
-character(len=:),allocatable :: bname          ! baeename of NAME
-character(len=:),allocatable :: message(:)
-character(len=:),allocatable :: littlefile(:)
-
-    call mkdir(settings%name)      ! make new directory
-    call run('cd '//settings%name) ! change to new directory as a test. New OS routines to improve this; system dependent potentially
-    !! NOTE: need some system routines to handle filenames like "." like realpath() or getcwd().
-    bname=basename(settings%name)
-
-    !! weird gfortran bug?? lines truncated to concatenated string length, not 80
-    !! hit some weird gfortran bug when littlefile data was an argument to warnwrite(3f), ok when a variable
-
-    call warnwrite(join_path(settings%name, '.gitignore'), ['build/*'])        ! create NAME/.gitignore file
-
-    littlefile=[character(len=80) :: '# '//bname, 'My cool new project!']
-
-    call warnwrite(join_path(settings%name, 'README.md'), littlefile)          ! create NAME/README.md
-
-    message=[character(len=80) ::             &                                ! start building NAME/fpm.toml
-    &'name = "'//bname//'"                 ', &
-    &'version = "0.1.0"                    ', &
-    &'license = "license"                  ', &
-    &'author = "Jane Doe"                  ', &
-    &'maintainer = "jane.doe@example.com"  ', &
-    &'copyright = "2020 Jane Doe"          ', &
-    &'                                     ', &
-    &'']
-
-    if(settings%with_lib)then
-        call mkdir(join_path(settings%name,'src') )
-        message=[character(len=80) ::  message,   &                             ! create next section of fpm.toml
-        &'[library]                            ', &
-        &'source-dir="src"                     ', &
-        &'']
-        littlefile=[character(len=80) ::          &                             ! create placeholder module src/bname.f90
-        &'module '//bname,                        &
-        &'  implicit none',                       &
-        &'  private',                             &
-        &'',                                      &
-        &'  public :: say_hello',                 &
-        &'contains',                              &
-        &'  subroutine say_hello',                &
-        &'    print *, "Hello, '//bname//'!"',    &
-        &'  end subroutine say_hello',            &
-        &'end module '//bname]
-       ! a proposed alternative default
-        call warnwrite(join_path(settings%name, 'src', bname//'.f90'), littlefile) ! create NAME/src/NAME.f90
-    endif
-
-    if(settings%with_test)then
-        call mkdir(join_path(settings%name, 'test'))                            ! create NAME/test or stop
-        message=[character(len=80) ::  message,   &                             ! create next section of fpm.toml
-        &'[[test]]                             ', &
-        &'name="runTests"                      ', &
-        &'source-dir="test"                    ', &
-        &'main="main.f90"                      ', &
-        &'']
-  
-        littlefile=[character(len=80) ::        &
-        &'program main',                       &
-        &'implicit none',                      &
-        &'',                                   &
-        &'print *, "Put some tests in here!"', &
-        &'end program main']
-        ! a proposed alternative default a little more substantive
-        call warnwrite(join_path(settings%name, 'test/main.f90'), littlefile)    ! create NAME/test/main.f90
-    endif
-
-    if(settings%with_executable)then
-        call mkdir(join_path(settings%name, 'app'))                             ! create NAME/app or stop
-        message=[character(len=80) ::  message,   &                             ! create next section of fpm.toml
-        &'[[executable]]                       ', &
-        &'name="'//bname//'"                   ', &
-        &'source-dir="app"                     ', &
-        &'main="main.f90"                      ', &
-        &'']
-
-        littlefile=[character(len=80) ::          &
-        &'program main',                          &
-        &'  use '//bname//', only: say_hello',    &
-        &'',                                      &
-        &'  implicit none',                       &
-        &'',                                      &
-        &'  call say_hello',                      &
-        &'end program main']
-        call warnwrite(join_path(settings%name, 'app/main.f90'), littlefile)
-    endif
-
-    call warnwrite(join_path(settings%name, 'fpm.toml'), message)               ! now that built it write NAME/fpm.toml
-
-    call run('cd ' // settings%name // ';git init')    ! assumes these commands work on all systems and git(1) is installed
-contains
-
-subroutine warnwrite(fname,data)
-character(len=*),intent(in) :: fname
-character(len=*),intent(in) :: data(:)
-
-    if(.not.exists(fname))then
-       call filewrite(fname,data)
-    else
-       write(stderr,'(*(g0,1x))')'fpm::new<WARNING>',fname,'already exists. Not overwriting'
-    endif
-
-end subroutine warnwrite
-
-subroutine filewrite(filename,filedata)
-use,intrinsic :: iso_fortran_env, only : stdin=>input_unit, stdout=>output_unit, stderr=>error_unit
-! write filedata to file filename
-character(len=*),intent(in)           :: filename
-character(len=*),intent(in)           :: filedata(:)
-integer                               :: lun, i, ios
-character(len=256)                    :: message
-
-    message=' '
-    ios=0
-    if(filename.ne.' ')then
-        open(file=filename, &
-        & newunit=lun, &
-        & form='formatted', &      !  FORM      =  FORMATTED   |  UNFORMATTED
-        & access='sequential', &   !  ACCESS    =  SEQUENTIAL  |  DIRECT       |  STREAM
-        & action='write', &        !  ACTION    =  READ|WRITE  |  READWRITE
-        & position='rewind', &     !  POSITION  =  ASIS        |  REWIND       |  APPEND
-        & status='new', &          !  STATUS    =  NEW         |  REPLACE      |  OLD     |  SCRATCH   | UNKNOWN
-        & iostat=ios, &
-        & iomsg=message)
-    else
-        lun=stdout
-        ios=0
-    endif
-    if(ios.ne.0)then
-        write(stderr,'(*(a:,1x))')'*filewrite* error:',filename,trim(message)
-        error stop 1
-    endif
-    do i=1,size(filedata)                                                    ! write file
-        write(lun,'(a)',iostat=ios,iomsg=message)trim(filedata(i))
-        if(ios.ne.0)then
-            write(stderr,'(*(a:,1x))')'*filewrite* error:',filename,trim(message)
-            error stop 4
-        endif
-    enddo
-    close(unit=lun,iostat=ios,iomsg=message)                                 ! close file
-    if(ios.ne.0)then
-        write(stderr,'(*(a:,1x))')'*filewrite* error:',trim(message)
-        error stop 2
-    endif
-end subroutine filewrite
-
-end subroutine cmd_new
-
-
 subroutine cmd_run(settings)
 type(fpm_run_settings), intent(in) :: settings
 character(len=:),allocatable       :: release_name, cmd, fname
diff --git a/fpm/src/fpm/cmd/new.f90 b/fpm/src/fpm/cmd/new.f90
new file mode 100644
index 0000000..fc4c93e
--- /dev/null
+++ b/fpm/src/fpm/cmd/new.f90
@@ -0,0 +1,164 @@
+module fpm_cmd_new
+
+use fpm_command_line, only : fpm_new_settings
+use fpm_environment, only : run, OS_LINUX, OS_MACOS, OS_WINDOWS
+use fpm_filesystem, only : join_path, exists, basename, mkdir
+use,intrinsic :: iso_fortran_env, only : stderr=>error_unit
+implicit none
+private
+public :: cmd_new
+
+contains
+
+subroutine cmd_new(settings) ! --with-executable F --with-test F '
+type(fpm_new_settings), intent(in) :: settings
+character(len=:),allocatable :: bname          ! baeename of NAME
+character(len=:),allocatable :: message(:)
+character(len=:),allocatable :: littlefile(:)
+
+    call mkdir(settings%name)      ! make new directory
+    call run('cd '//settings%name) ! change to new directory as a test. System dependent potentially
+    !! NOTE: need some system routines to handle filenames like "." like realpath() or getcwd().
+    bname=basename(settings%name)
+
+    !! weird gfortran bug?? lines truncated to concatenated string length, not 80
+    !! hit some weird gfortran bug when littlefile data was an argument to warnwrite(3f), ok when a variable
+
+    call warnwrite(join_path(settings%name, '.gitignore'), ['build/*'])        ! create NAME/.gitignore file
+
+    littlefile=[character(len=80) :: '# '//bname, 'My cool new project!']
+
+    call warnwrite(join_path(settings%name, 'README.md'), littlefile)          ! create NAME/README.md
+
+    message=[character(len=80) ::             &                                ! start building NAME/fpm.toml
+    &'name = "'//bname//'"                 ', &
+    &'version = "0.1.0"                    ', &
+    &'license = "license"                  ', &
+    &'author = "Jane Doe"                  ', &
+    &'maintainer = "jane.doe@example.com"  ', &
+    &'copyright = "2020 Jane Doe"          ', &
+    &'                                     ', &
+    &'']
+
+    if(settings%with_lib)then
+        call mkdir(join_path(settings%name,'src') )
+        message=[character(len=80) ::  message,   &                             ! create next section of fpm.toml
+        &'[library]                            ', &
+        &'source-dir="src"                     ', &
+        &'']
+        littlefile=[character(len=80) ::          &                             ! create placeholder module src/bname.f90
+        &'module '//bname,                        &
+        &'  implicit none',                       &
+        &'  private',                             &
+        &'',                                      &
+        &'  public :: say_hello',                 &
+        &'contains',                              &
+        &'  subroutine say_hello',                &
+        &'    print *, "Hello, '//bname//'!"',    &
+        &'  end subroutine say_hello',            &
+        &'end module '//bname]
+       ! a proposed alternative default
+        call warnwrite(join_path(settings%name, 'src', bname//'.f90'), littlefile) ! create NAME/src/NAME.f90
+    endif
+
+    if(settings%with_test)then
+        call mkdir(join_path(settings%name, 'test'))                            ! create NAME/test or stop
+        message=[character(len=80) ::  message,   &                             ! create next section of fpm.toml
+        &'[[test]]                             ', &
+        &'name="runTests"                      ', &
+        &'source-dir="test"                    ', &
+        &'main="main.f90"                      ', &
+        &'']
+
+        littlefile=[character(len=80) ::        &
+        &'program main',                       &
+        &'implicit none',                      &
+        &'',                                   &
+        &'print *, "Put some tests in here!"', &
+        &'end program main']
+        ! a proposed alternative default a little more substantive
+        call warnwrite(join_path(settings%name, 'test/main.f90'), littlefile)    ! create NAME/test/main.f90
+    endif
+
+    if(settings%with_executable)then
+        call mkdir(join_path(settings%name, 'app'))                             ! create NAME/app or stop
+        message=[character(len=80) ::  message,   &                             ! create next section of fpm.toml
+        &'[[executable]]                       ', &
+        &'name="'//bname//'"                   ', &
+        &'source-dir="app"                     ', &
+        &'main="main.f90"                      ', &
+        &'']
+
+        littlefile=[character(len=80) ::          &
+        &'program main',                          &
+        &'  use '//bname//', only: say_hello',    &
+        &'',                                      &
+        &'  implicit none',                       &
+        &'',                                      &
+        &'  call say_hello',                      &
+        &'end program main']
+        call warnwrite(join_path(settings%name, 'app/main.f90'), littlefile)
+    endif
+
+    call warnwrite(join_path(settings%name, 'fpm.toml'), message)               ! now that built it write NAME/fpm.toml
+
+    call run('cd ' // settings%name // '&&git init')    ! assumes these commands work on all systems and git(1) is installed
+contains
+
+subroutine warnwrite(fname,data)
+character(len=*),intent(in) :: fname
+character(len=*),intent(in) :: data(:)
+
+    if(.not.exists(fname))then
+       call filewrite(fname,data)
+    else
+       write(stderr,'(*(g0,1x))')'fpm::new<WARNING>',fname,'already exists. Not overwriting'
+    endif
+
+end subroutine warnwrite
+
+subroutine filewrite(filename,filedata)
+use,intrinsic :: iso_fortran_env, only : stdin=>input_unit, stdout=>output_unit, stderr=>error_unit
+! write filedata to file filename
+character(len=*),intent(in)           :: filename
+character(len=*),intent(in)           :: filedata(:)
+integer                               :: lun, i, ios
+character(len=256)                    :: message
+
+    message=' '
+    ios=0
+    if(filename.ne.' ')then
+        open(file=filename, &
+        & newunit=lun, &
+        & form='formatted', &      !  FORM      =  FORMATTED   |  UNFORMATTED
+        & access='sequential', &   !  ACCESS    =  SEQUENTIAL  |  DIRECT       |  STREAM
+        & action='write', &        !  ACTION    =  READ|WRITE  |  READWRITE
+        & position='rewind', &     !  POSITION  =  ASIS        |  REWIND       |  APPEND
+        & status='new', &          !  STATUS    =  NEW         |  REPLACE      |  OLD     |  SCRATCH   | UNKNOWN
+        & iostat=ios, &
+        & iomsg=message)
+    else
+        lun=stdout
+        ios=0
+    endif
+    if(ios.ne.0)then
+        write(stderr,'(*(a:,1x))')'*filewrite* error:',filename,trim(message)
+        error stop 1
+    endif
+    do i=1,size(filedata)                                                    ! write file
+        write(lun,'(a)',iostat=ios,iomsg=message)trim(filedata(i))
+        if(ios.ne.0)then
+            write(stderr,'(*(a:,1x))')'*filewrite* error:',filename,trim(message)
+            error stop 4
+        endif
+    enddo
+    close(unit=lun,iostat=ios,iomsg=message)                                 ! close file
+    if(ios.ne.0)then
+        write(stderr,'(*(a:,1x))')'*filewrite* error:',trim(message)
+        error stop 2
+    endif
+end subroutine filewrite
+
+end subroutine cmd_new
+
+end module fpm_cmd_new
diff --git a/fpm/src/fpm/git.f90 b/fpm/src/fpm/git.f90
index 28ae867..187b551 100644
--- a/fpm/src/fpm/git.f90
+++ b/fpm/src/fpm/git.f90
@@ -1,5 +1,6 @@
 !> Implementation for interacting with git repositories.
 module fpm_git
+    use fpm_error, only: error_t, fatal_error
     implicit none
 
     public :: git_target_t
@@ -43,6 +44,9 @@ module fpm_git
 
     contains
 
+        !> Fetch and checkout in local directory
+        procedure :: checkout
+
         !> Show information on instance
         procedure :: info
 
@@ -124,6 +128,54 @@ contains
     end function git_target_tag
 
 
+    subroutine checkout(self,local_path, error)
+
+        !> Instance of the git target
+        class(git_target_t), intent(in) :: self
+
+        !> Local path to checkout in
+        character(*), intent(in) :: local_path
+
+        !> Error
+        type(error_t), allocatable, intent(out) :: error
+        
+        !> git object ref
+        character(:), allocatable :: object
+
+        !> Stat for execute_command_line
+        integer :: stat
+
+        if (allocated(self%object)) then
+            object = self%object
+        else
+            object = 'HEAD'
+        end if
+
+        call execute_command_line("git init "//local_path, exitstat=stat)
+
+        if (stat /= 0) then
+            call fatal_error(error,'Error while initiating git repository for remote dependency')
+            return
+        end if
+
+        call execute_command_line("git -C "//local_path//" fetch "//self%url//&
+                                        " "//object, exitstat=stat)
+
+        if (stat /= 0) then
+            call fatal_error(error,'Error while fetching git repository for remote dependency')
+            return
+        end if
+
+        call execute_command_line("git -C "//local_path//" checkout -qf FETCH_HEAD", exitstat=stat)
+
+        if (stat /= 0) then
+            call fatal_error(error,'Error while checking out git repository for remote dependency')
+            return
+        end if
+
+    end subroutine checkout 
+
+
     !> Show information on git target
     subroutine info(self, unit, verbosity)
 
diff --git a/fpm/src/fpm_backend.f90 b/fpm/src/fpm_backend.f90
index 40460d7..d7005bf 100644
--- a/fpm/src/fpm_backend.f90
+++ b/fpm/src/fpm_backend.f90
@@ -3,7 +3,7 @@ module fpm_backend
 ! Implements the native fpm build backend
 
 use fpm_environment, only: run, get_os_type, OS_WINDOWS
-use fpm_filesystem, only: basename, join_path, exists, mkdir
+use fpm_filesystem, only: basename, dirname, join_path, exists, mkdir
 use fpm_model, only: fpm_model_t, srcfile_t, FPM_UNIT_MODULE, &
                      FPM_UNIT_SUBMODULE, FPM_UNIT_SUBPROGRAM, &
                      FPM_UNIT_CSOURCE, FPM_UNIT_PROGRAM, &
@@ -113,6 +113,10 @@ recursive subroutine build_source(model,source_file,linking)
 
     object_file = get_object_name(model,source_file%file_name)
     
+    if (.not.exists(dirname(object_file))) then
+        call mkdir(dirname(object_file))
+    end if
+
     call run("gfortran -c " // source_file%file_name // model%fortran_compile_flags &
               // " -o " // object_file)
     linking = linking // " " // object_file
@@ -145,13 +149,6 @@ function get_object_name(model,source_file_name) result(object_file)
     ! Exclude first directory level from path
     object_file = source_file_name(index(source_file_name,filesep)+1:)
 
-    ! Convert remaining directory separators to underscores
-    i = index(object_file,filesep)
-    do while(i > 0)
-        object_file(i:i) = '_'
-        i = index(object_file,filesep)
-    end do
-
     ! Construct full target path
     object_file = join_path(model%output_directory, model%package_name, &
                         object_file//'.o')
diff --git a/fpm/src/fpm_command_line.f90 b/fpm/src/fpm_command_line.f90
index 5b9d93a..1a7e4ab 100644
--- a/fpm/src/fpm_command_line.f90
+++ b/fpm/src/fpm_command_line.f90
@@ -416,8 +416,9 @@ contains
     '                                                                ', &
     ' The "new" subcommand creates a directory and runs the command  ', &
     ' "git init" in that directory and makes an example "fpm.toml"   ', &
-    ' file, a src/ directory, and optionally a test/ and app/        ', &
-    ' directory with trivial example Fortran source files.           ', &
+    ' file. and src/ directory and a sample module file. It          ', &
+    ' optionally also creates a test/ and app/ directory with        ', &
+    ' trivial example Fortran program sources.                       ', &
     '                                                                ', &
     ' Remember to update the information in the sample "fpm.toml"    ', &
     ' file with such information as your name and e-mail address.    ', &
diff --git a/fpm/src/fpm_filesystem.f90 b/fpm/src/fpm_filesystem.f90
index d2096f1..4c12314 100644
--- a/fpm/src/fpm_filesystem.f90
+++ b/fpm/src/fpm_filesystem.f90
@@ -215,6 +215,8 @@ subroutine mkdir(dir)
     character(len=*), intent(in) :: dir
     integer                      :: stat
 
+    if (is_dir(dir)) return
+
     select case (get_os_type())
         case (OS_UNKNOWN, OS_LINUX, OS_MACOS, OS_CYGWIN, OS_SOLARIS, OS_FREEBSD)
             call execute_command_line('mkdir -p ' // dir, exitstat=stat)
@@ -233,6 +235,11 @@ end subroutine mkdir
 
 
 recursive subroutine list_files(dir, files, recurse)
+    ! Get file & directory names in directory `dir`.
+    !
+    !  - File/directory names return are relative to cwd, ie. preprended with `dir`
+    !  - Includes files starting with `.` except current directory and parent directory
+    !
     character(len=*), intent(in) :: dir
     type(string_t), allocatable, intent(out) :: files(:)
     logical, intent(in), optional :: recurse
@@ -242,8 +249,7 @@ recursive subroutine list_files(dir, files, recurse)
     type(string_t), allocatable :: dir_files(:)
     type(string_t), allocatable :: sub_dir_files(:)
 
-    ! Using `inquire` / exists on directories works with gfortran, but not ifort
-    if (.not. exists(dir)) then
+    if (.not. is_dir(dir)) then
         allocate (files(0))
         return
     end if
@@ -252,7 +258,7 @@ recursive subroutine list_files(dir, files, recurse)
 
     select case (get_os_type())
         case (OS_UNKNOWN, OS_LINUX, OS_MACOS, OS_CYGWIN, OS_SOLARIS, OS_FREEBSD)
-            call execute_command_line('ls ' // dir // ' > ' // temp_file, &
+            call execute_command_line('ls -A ' // dir // ' > ' // temp_file, &
                                       exitstat=stat)
         case (OS_WINDOWS)
             call execute_command_line('dir /b ' // windows_path(dir) // ' > ' // temp_file, &
diff --git a/fpm/src/fpm_sources.f90 b/fpm/src/fpm_sources.f90
index f798276..393c799 100644
--- a/fpm/src/fpm_sources.f90
+++ b/fpm/src/fpm_sources.f90
@@ -6,7 +6,7 @@ use fpm_model, only: srcfile_ptr, srcfile_t, fpm_model_t, &
                     FPM_UNIT_CSOURCE, FPM_UNIT_CHEADER, FPM_SCOPE_UNKNOWN, &
                     FPM_SCOPE_LIB, FPM_SCOPE_DEP, FPM_SCOPE_APP, FPM_SCOPE_TEST
                     
-use fpm_filesystem, only: basename, canon_path, dirname, read_lines, list_files
+use fpm_filesystem, only: basename, canon_path, dirname, join_path, read_lines, list_files
 use fpm_strings, only: lower, split, str_ends_with, string_t, operator(.in.)
 use fpm_manifest_executable, only: executable_t
 implicit none
@@ -24,6 +24,33 @@ character(15), parameter :: INTRINSIC_MODULE_NAMES(*) =  &
 
 contains
 
+function parse_source(source_file_path,error) result(source)
+    character(*), intent(in) :: source_file_path
+    type(error_t), allocatable, intent(out) :: error
+    type(srcfile_t)  :: source
+
+    if (str_ends_with(lower(source_file_path), ".f90")) then
+
+        source = parse_f_source(source_file_path, error)
+
+        if (source%unit_type == FPM_UNIT_PROGRAM) then
+            source%exe_name = basename(source_file_path,suffix=.false.)
+        end if
+
+    else if (str_ends_with(lower(source_file_path), ".c") .or. &
+        str_ends_with(lower(source_file_path), ".h")) then
+
+        source = parse_c_source(source_file_path,error)
+
+    end if
+
+    if (allocated(error)) then
+        return
+    end if
+
+end function parse_source
+
+
 subroutine add_sources_from_dir(sources,directory,scope,with_executables,error)
     ! Enumerate sources in a directory
     !
@@ -33,7 +60,7 @@ subroutine add_sources_from_dir(sources,directory,scope,with_executables,error)
     logical, intent(in), optional :: with_executables
     type(error_t), allocatable, intent(out) :: error
 
-    integer :: i, j
+    integer :: i
     logical, allocatable :: is_source(:), exclude_source(:)
     type(string_t), allocatable :: file_names(:)
     type(string_t), allocatable :: src_file_names(:)
@@ -46,13 +73,13 @@ subroutine add_sources_from_dir(sources,directory,scope,with_executables,error)
     if (allocated(sources)) then
         allocate(existing_src_files(size(sources)))
         do i=1,size(sources)
-            existing_src_files(i)%s = sources(i)%file_name
+            existing_src_files(i)%s = canon_path(sources(i)%file_name)
         end do
     else
         allocate(existing_src_files(0))
     end if
 
-    is_source = [(.not.(file_names(i)%s .in. existing_src_files) .and. &
+    is_source = [(.not.(canon_path(file_names(i)%s) .in. existing_src_files) .and. &
                   (str_ends_with(lower(file_names(i)%s), ".f90") .or. &
                    str_ends_with(lower(file_names(i)%s), ".c") .or. &
                    str_ends_with(lower(file_names(i)%s), ".h") ),i=1,size(file_names))]
@@ -63,26 +90,8 @@ subroutine add_sources_from_dir(sources,directory,scope,with_executables,error)
 
     do i = 1, size(src_file_names)
 
-        if (str_ends_with(lower(src_file_names(i)%s), ".f90")) then
-
-            dir_sources(i) = parse_f_source(src_file_names(i)%s, error)
-
-            if (allocated(error)) then
-                return
-            end if
-
-        end if
-
-        if (str_ends_with(lower(src_file_names(i)%s), ".c") .or. &
-            str_ends_with(lower(src_file_names(i)%s), ".h")) then
-
-            dir_sources(i) = parse_c_source(src_file_names(i)%s,error)
-
-            if (allocated(error)) then
-                return
-            end if
-
-        end if
+        dir_sources(i) = parse_source(src_file_names(i)%s,error)
+        if (allocated(error)) return
 
         dir_sources(i)%unit_scope = scope
 
@@ -93,7 +102,6 @@ subroutine add_sources_from_dir(sources,directory,scope,with_executables,error)
             if (with_executables) then
 
                 exclude_source(i) = .false.
-                dir_sources(i)%exe_name = basename(src_file_names(i)%s,suffix=.false.)
 
             end if
         end if
@@ -122,49 +130,50 @@ subroutine add_executable_sources(sources,executables,scope,auto_discover,error)
     integer :: i, j
 
     type(string_t), allocatable :: exe_dirs(:)
-    logical, allocatable :: include_source(:)
-    type(srcfile_t), allocatable :: dir_sources(:)
+    type(srcfile_t) :: exe_source
 
     call get_executable_source_dirs(exe_dirs,executables)
 
     do i=1,size(exe_dirs)
-        call add_sources_from_dir(dir_sources,exe_dirs(i)%s, &
-                     scope, with_executables=.true.,error=error)
+        call add_sources_from_dir(sources,exe_dirs(i)%s, &
+                     scope, with_executables=auto_discover,error=error)
 
         if (allocated(error)) then
             return
         end if
     end do
 
-    allocate(include_source(size(dir_sources)))
+    exe_loop: do i=1,size(executables)
 
-    do i = 1, size(dir_sources)
-        
-        ! Include source by default if not a program or if auto_discover is enabled
-        include_source(i) = (dir_sources(i)%unit_type /= FPM_UNIT_PROGRAM) .or. &
-                             auto_discover
+        ! Check if executable already discovered automatically
+        !  and apply any overrides
+        do j=1,size(sources)
 
-        ! Always include sources specified in fpm.toml
-        do j=1,size(executables)
-
-            if (basename(dir_sources(i)%file_name,suffix=.true.) == executables(j)%main .and.&
-                 canon_path(dirname(dir_sources(i)%file_name)) == &
-                 canon_path(executables(j)%source_dir) ) then
+            if (basename(sources(j)%file_name,suffix=.true.) == executables(i)%main .and.&
+                 canon_path(dirname(sources(j)%file_name)) == &
+                 canon_path(executables(i)%source_dir) ) then
                 
-                include_source(i) = .true.
-                dir_sources(i)%exe_name = executables(j)%name
-                exit
+                sources(j)%exe_name = executables(i)%name
+                cycle exe_loop
 
             end if
+
         end do
 
-    end do
+        ! Add if not already discovered (auto_discovery off)
+        exe_source = parse_source(join_path(executables(i)%source_dir,executables(i)%main),error)
+        exe_source%exe_name = executables(i)%name
+        exe_source%unit_scope = scope
+        
+        if (allocated(error)) return
 
-    if (.not.allocated(sources)) then
-        sources = pack(dir_sources,include_source)
-    else
-        sources = [sources, pack(dir_sources,include_source)]
-    end if
+        if (.not.allocated(sources)) then
+            sources = [exe_source]
+        else
+            sources = [sources, exe_source]
+        end if
+
+    end do exe_loop
 
 end subroutine add_executable_sources
 
@@ -291,21 +300,26 @@ function parse_f_source(f_filename,error) result(f_source)
             end if
 
             ! Process 'INCLUDE' statements
-            if (index(adjustl(lower(file_lines(i)%s)),'include') == 1) then
-    
-                n_include = n_include + 1
+            ic = index(adjustl(lower(file_lines(i)%s)),'include')
+            if ( ic == 1 ) then
+                ic = index(lower(file_lines(i)%s),'include')
+                if (index(adjustl(file_lines(i)%s(ic+7:)),'"') == 1 .or. &
+                    index(adjustl(file_lines(i)%s(ic+7:)),"'") == 1 ) then
 
-                if (pass == 2) then
-                    f_source%include_dependencies(n_include)%s = &
-                     & split_n(file_lines(i)%s,n=2,delims="'"//'"',stat=stat)
-                    if (stat /= 0) then
-                        call file_parse_error(error,f_filename, &
-                              'unable to find include file name',i, &
-                              file_lines(i)%s)
-                        return
+    
+                    n_include = n_include + 1
+
+                    if (pass == 2) then
+                        f_source%include_dependencies(n_include)%s = &
+                         & split_n(file_lines(i)%s,n=2,delims="'"//'"',stat=stat)
+                        if (stat /= 0) then
+                            call file_parse_error(error,f_filename, &
+                                  'unable to find include file name',i, &
+                                  file_lines(i)%s)
+                            return
+                        end if
                     end if
                 end if
-
             end if
 
             ! Extract name of module if is module
diff --git a/fpm/test/cli_test/cli_test.f90 b/fpm/test/cli_test/cli_test.f90
index fac49e8..b0140e1 100644
--- a/fpm/test/cli_test/cli_test.f90
+++ b/fpm/test/cli_test/cli_test.f90
@@ -193,7 +193,8 @@ use fpm_command_line, only: &
         fpm_test_settings, &
         fpm_install_settings, &
         get_command_line_settings
-use fpm, only: cmd_build, cmd_install, cmd_new, cmd_run, cmd_test
+use fpm, only: cmd_build, cmd_install, cmd_run, cmd_test
+use fpm_cmd_new, only: cmd_new 
 class(fpm_cmd_settings), allocatable :: cmd_settings
 ! duplicates the calls as seen in the main program for fpm
 call get_command_line_settings(cmd_settings)
diff --git a/fpm/test/fpm_test/test_source_parsing.f90 b/fpm/test/fpm_test/test_source_parsing.f90
index 0b92bef..d1d3e12 100644
--- a/fpm/test/fpm_test/test_source_parsing.f90
+++ b/fpm/test/fpm_test/test_source_parsing.f90
@@ -198,9 +198,11 @@ contains
         write(unit, '(a)') &
             & 'program test', &
             & ' implicit none', &
-            & ' include "included_file.f90"', &
+            & ' include  "included_file.f90"', &
+            & ' character(*) :: include_comments', &
+            & ' include_comments = "some comments"', &
             & ' contains ', &
-            & '  include "second_include.f90"', &
+            & '  include"second_include.f90"', &
             & 'end program test'
         close(unit)