[mateusz-olczyk]

The File API reports sources[].path relative to the top-level source directory (codemodel.paths.source, i.e. cmake -S) whenever the file is inside it, and absolute otherwise. extract_cmake passed those paths through unchanged, and reconstruct only rebases absolute paths onto <repo_root>.

This is fine when -S is the repo root, but when the CMake project lives in a subdirectory of the Bazel workspace (cmake -S sub/proj), TU keys came out as src/a.c instead of sub/proj/src/a.c. Those sources then looked missing on the CMake side and extra on the Bazel side, even though both builds compiled the same files. Only sources under the project dir were affected; sources outside it were already reported absolute and keyed correctly, so a target could show a mix of correct and bogus keys.

extract_cmake now makes source paths absolute against codemodel.paths.source (falling back to <repo_root> for replies without paths), in both the synthesized -c argument and the action inputs. Repo-relative keying then works as it already does for include directories. Out-of-tree absolute sources are unchanged.

A new extractor test covers a project configured from a subdirectory with one in-tree and one out-of-tree source; it fails without the fix. docs/REFERENCE-cmake.md notes that -S may be any directory under <repo_root>.