Merge branch 'master' into bootstrap_submodule_support

13 files changed, 479 insertions, 249 deletions

diff --git a/ci/run_tests.bat b/ci/run_tests.bat
index 4136924..517ff06 100755
--- a/ci/run_tests.bat
+++ b/ci/run_tests.bat
@@ -25,6 +25,30 @@ if errorlevel 1 exit 1
 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
 
diff --git a/ci/run_tests.sh b/ci/run_tests.sh
index cde5645..4ba590a 100755
--- a/ci/run_tests.sh
+++ b/ci/run_tests.sh
@@ -12,6 +12,16 @@ 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
 ./build/gfortran_debug/app/say_Hello
diff --git a/example_packages/README.md b/example_packages/README.md
index 79fadb1..65f4109 100644
--- a/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/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/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/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_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)