Use correct subdir when generating processed file path

We need the subdir of where the output file will actually be created,
not the current subdir of the interpreter.

Fixes: mesonbuild#13168

mesonbuild/build.py

@@ -1823,8 +1823,7 @@ def process_files(self, files: T.Iterable[T.Union[str, File, 'CustomTarget', 'Cu
             if isinstance(e, CustomTargetIndex):
                 output.depends.add(e.target)
             if isinstance(e, (CustomTarget, CustomTargetIndex)):
-                output.depends.add(e)
-                fs = [File.from_built_file(state.subdir, f) for f in e.get_outputs()]
+                fs = [File.from_built_file(e.get_subdir(), f) for f in e.get_outputs()]
             elif isinstance(e, GeneratedList):
                 if preserve_path_from:
                     raise InvalidArguments("generator.process: 'preserve_path_from' is not allowed if one input is a 'generated_list'.")

test cases/common/276 generator custom_tgt subdir/include/meson.build

@@ -0,0 +1,4 @@
+test_header = custom_target(
+  output: 'test_header.h',
+  command: [touch, '@OUTPUT@'],
+)

test cases/common/276 generator custom_tgt subdir/meson.build

@@ -0,0 +1,22 @@
+project('276 generator custom_tgt subdir')
+
+touch = find_program('touch', required: false)
+if not touch.found()
+  error('MESON_SKIP_TEST: touch is required to run the test')
+endif
+
+subdir('include')
+
+gen = generator(
+  touch,
+  arguments: ['@OUTPUT@'],
+  output: '@[email protected]',
+)
+
+custom_target(
+  'check-headers.stamp',
+  command: [touch, '@INPUT@'],
+  input: gen.process(test_header),
+  output: 'check-headers.stamp',
+  build_by_default: true,
+)