Exempt Office/Workspace sidecars from the ignore check

detect() converts Office files and Google Workspace shortcuts into
markdown sidecars under a converted subdirectory of the output dir,
then ran the same scan ignore check on the sidecar's own path. The
documented gitignore advice puts the whole output dir inside a
gitignored tree, so that check rejected the tool's own output for
the same reason a user would gitignore it, and the source document
vanished from the corpus with nothing recorded about why. The check
exists to keep user files out of the scan, not to filter output this
same pass just produced from an already admitted source, so a
sidecar under the converted directory is now exempt from it. Fixes
#3504.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017qfdzgbA5KedGEjD1AayNh
(cherry picked from commit 900b376d39)

graphify/detect.py

@@ -1968,7 +1968,15 @@ def detect(root: Path, *, follow_symlinks: bool | None = None, google_workspace:
                     skipped_sensitive.append(str(p) + f" [Google Workspace export failed: {exc}]")
                     continue
                 if md_path:
-                    if _ignored_for_scan(md_path):
+                    # #3504: the sidecar lands under converted_dir, which the
+                    # documented .gitignore advice puts inside a gitignored
+                    # graphify-out/ -- an ignore check here would reject the
+                    # tool's own output for the same reason it should be
+                    # gitignored in the first place, silently dropping the
+                    # source document from the corpus. The ignore check exists
+                    # to keep USER files out of the scan, not to filter output
+                    # this same pass just produced from an already-admitted file.
+                    if _ignored_for_scan(md_path) and not md_path.is_relative_to(converted_dir):
                         continue
                     files[ftype].append(str(md_path))
                     total_words += _wc(md_path)
@@ -1979,7 +1987,10 @@ def detect(root: Path, *, follow_symlinks: bool | None = None, google_workspace:
             if p.suffix.lower() in OFFICE_EXTENSIONS:
                 md_path = convert_office_file(p, converted_dir, root=root)
                 if md_path:
-                    if _ignored_for_scan(md_path):
+                    # #3504: see the matching comment in the Google Workspace
+                    # branch above -- same sidecar-under-a-gitignored-output-dir
+                    # trap, same exemption.
+                    if _ignored_for_scan(md_path) and not md_path.is_relative_to(converted_dir):
                         continue
                     files[ftype].append(str(md_path))
                     total_words += _wc(md_path)

tests/test_detect.py

@@ -872,6 +872,58 @@ def test_detect_converts_google_workspace_shortcuts_when_enabled(tmp_path, monke
     assert result["total_words"] > 0
 
 
+def test_detect_office_sidecar_survives_a_gitignored_output_dir(tmp_path, monkeypatch):
+    """#3504: the documented .gitignore advice puts graphify-out/ (and so
+    graphify-out/converted/, where Office sidecars land) inside a gitignored
+    tree. The ignore check exists to keep USER files out of the scan, not to
+    filter output this same pass just produced from an already-admitted
+    source file -- so a sidecar landing under converted/ must survive it,
+    or every .docx/.xlsx silently vanishes from the corpus the moment a repo
+    follows that advice."""
+    (tmp_path / ".gitignore").write_text("graphify-out/\n", encoding="utf-8")
+    src = tmp_path / "report.docx"
+    src.write_text("placeholder", encoding="utf-8")
+
+    def fake_convert(path, out_dir, root=None):
+        out_dir.mkdir(parents=True, exist_ok=True)
+        out = out_dir / "report_converted.md"
+        out.write_text("# Report\n\nConverted content.", encoding="utf-8")
+        return out
+
+    monkeypatch.setattr("graphify.detect.convert_office_file", fake_convert)
+
+    result = detect(tmp_path)
+
+    assert len(result["files"]["document"]) == 1, (
+        "the Office sidecar was dropped by the gitignore check on the tool's own output dir"
+    )
+    assert result["files"]["document"][0].endswith("report_converted.md")
+    assert result["total_words"] > 0
+
+
+def test_detect_google_workspace_sidecar_survives_a_gitignored_output_dir(tmp_path, monkeypatch):
+    """Same trap as the Office sidecar case (#3504), for the Google Workspace
+    conversion branch, which writes into the same converted/ directory."""
+    (tmp_path / ".gitignore").write_text("graphify-out/\n", encoding="utf-8")
+    shortcut = tmp_path / "notes.gdoc"
+    shortcut.write_text('{"doc_id":"doc-1"}', encoding="utf-8")
+
+    def fake_convert(path, out_dir, *, xlsx_to_markdown=None, root=None):
+        out_dir.mkdir(parents=True, exist_ok=True)
+        out = out_dir / "notes_converted.md"
+        out.write_text("# Notes\n\nA converted Google Doc.", encoding="utf-8")
+        return out
+
+    monkeypatch.setattr("graphify.detect.convert_google_workspace_file", fake_convert)
+
+    result = detect(tmp_path, google_workspace=True)
+
+    assert len(result["files"]["document"]) == 1, (
+        "the Google Workspace sidecar was dropped by the gitignore check on the tool's own output dir"
+    )
+    assert result["files"]["document"][0].endswith("notes_converted.md")
+
+
 def test_detect_includes_video_key(tmp_path):
     """detect() result always includes a 'video' key even with no video files."""
     (tmp_path / "main.py").write_text("x = 1")