diff --git a/mesonbuild/backend/ninjabackend.py b/mesonbuild/backend/ninjabackend.py
index fa537adca..fe3be4ce1 100644
--- a/mesonbuild/backend/ninjabackend.py
+++ b/mesonbuild/backend/ninjabackend.py
@@ -329,13 +329,14 @@ int dummy;
         generated_source_files = []
         for rel_src, gensrc in generated_sources.items():
             generated_output_sources.append(rel_src)
+            raw_src = RawFilename(rel_src)
             if self.environment.is_source(rel_src) and not self.environment.is_header(rel_src):
                 if is_unity:
-                    unity_deps.append(rel_src)
+                    unity_deps.append(raw_src)
                     abs_src = os.path.join(self.environment.get_build_dir(), rel_src)
                     unity_src.append(abs_src)
                 else:
-                    generated_source_files.append(RawFilename(rel_src))
+                    generated_source_files.append(raw_src)
             elif self.environment.is_object(rel_src):
                 obj_list.append(rel_src)
             elif self.environment.is_library(rel_src):
@@ -344,7 +345,7 @@ int dummy;
                 # Assume anything not specifically a source file is a header. This is because
                 # people generate files with weird suffixes (.inc, .fh) that they then include
                 # in their source files.
-                header_deps.append(RawFilename(rel_src))
+                header_deps.append(raw_src)
         # These are the generated source files that need to be built for use by
         # this target. We create the Ninja build file elements for this here
         # because we need `header_deps` to be fully generated in the above loop.
@@ -356,10 +357,11 @@ int dummy;
         # sources. This can be extended to other $LANG->C compilers later if
         # necessary. This needs to be separate for at least Vala
         for src in vala_generated_sources:
+            raw_src = RawFilename(src)
             src_list.append(src)
             if is_unity:
                 unity_src.append(os.path.join(self.environment.get_build_dir(), src))
-                header_deps.append(src)
+                header_deps.append(raw_src)
             else:
                 # Generated targets are ordered deps because the must exist
                 # before the sources compiling them are used. After the first
@@ -367,12 +369,12 @@ int dummy;
                 # This should work in all cases. If it does not, then just
                 # move them from orderdeps to proper deps.
                 if self.environment.is_header(src):
-                    header_deps.append(src)
+                    header_deps.append(raw_src)
                 else:
                     # Passing 'vala' here signifies that we want the compile
                     # arguments to be specialized for C code generated by
                     # valac. For instance, no warnings should be emitted.
-                    obj_list.append(self.generate_single_compile(target, outfile, src, 'vala', [], header_deps))
+                    obj_list.append(self.generate_single_compile(target, outfile, raw_src, 'vala', [], header_deps))
         # Generate compile targets for all the pre-existing sources for this target
         for f, src in target_sources.items():
             if not self.environment.is_header(src):
@@ -386,7 +388,7 @@ int dummy;
         obj_list += self.flatten_object_list(target)
         if is_unity:
             for src in self.generate_unity_files(target, unity_src):
-                obj_list.append(self.generate_single_compile(target, outfile, src, True, unity_deps + header_deps))
+                obj_list.append(self.generate_single_compile(target, outfile, RawFilename(src), True, unity_deps + header_deps))
         linker = self.determine_linker(target, src_list + generated_output_sources)
         elem = self.generate_link(target, outfile, outname, obj_list, linker, pch_objects)
         self.generate_shlib_aliases(target, self.get_target_dir(target))
@@ -1670,10 +1672,10 @@ rule FORTRAN_DEP_HACK
         """
         Compiles only C/C++ and ObjC/ObjC++ sources
         """
-        if(isinstance(src, str) and src.endswith('.h')):
-            raise RuntimeError('Fug')
+        if isinstance(src, str) and src.endswith('.h'):
+            raise AssertionError('BUG: sources should not contain headers')
         if isinstance(src, RawFilename) and src.fname.endswith('.h'):
-            raise RuntimeError('Fug')
+            raise AssertionError('BUG: sources should not contain headers')
         extra_orderdeps = []
         compiler = self.get_compiler_for_source(src, target.is_cross)
         commands = []
@@ -1716,12 +1718,12 @@ rule FORTRAN_DEP_HACK
                 break
         if isinstance(src, RawFilename):
             rel_src = src.fname
-        elif is_generated:
-            if self.has_dir_part(src):
-                rel_src = src
+            if os.path.isabs(src.fname):
+                abs_src = src.fname
             else:
-                rel_src = os.path.join(self.get_target_private_dir(target), src)
-                abs_src = os.path.join(self.environment.get_source_dir(), rel_src)
+                abs_src = os.path.join(self.environment.get_build_dir(), src.fname)
+        elif is_generated:
+            raise AssertionError('BUG: broken generated source file handling for {!r}'.format(src))
         else:
             if isinstance(src, File):
                 rel_src = src.rel_to_builddir(self.build_to_src)
@@ -1805,6 +1807,7 @@ rule FORTRAN_DEP_HACK
         return rel_obj
 
     def has_dir_part(self, fname):
+        # FIXME FIXME: The usage of this is a terrible and unreliable hack
         return '/' in fname or '\\' in fname
 
     # Fortran is a bit weird (again). When you link against a library, just compiling a source file