phase: 105_hidden_folders_toggle

All completion criteria verified. Everything is green.

**Phase 105 final verification pass — all criteria verified**

- Verified the full implementation in the working tree: `git_sources.include_hidden` column + alembic `0019` (dev DB at head, column present), `iter_importable_files`/`import_sources` flag support with `str(root)`-keyed map used by both walk and progress pre-walk, `GitSourcePatchIn` rename with optional fields, sync/CLI pipeline wiring (OR-collision), and the per-row "Hidden" checkbox + tag + error line on the Sources page
- Unit + integration: `uv run pytest` → exit 0 (2148 tests collected, all pass; this sandbox occasionally swallows pytest's final status line — exit codes verified)
- Coverage: `uv run pytest --cov=app --cov-report=term-missing` → **TOTAL 99%** (3879 stmts, 15 miss) — >90% gate ✓
- Dedicated E2E: `uv run pytest tests/e2e/test_hidden_folders_toggle.py -v --no-cov` → **6 passed in 23.20s** (DB up, in isolation)
- Regression E2E in isolation: `test_source_ignore_paths` 6 passed, `test_git_sources_admin` 6 passed, `test_local_directory_sources` 3 passed, `test_sync_button` 3 passed, `test_smoke` 3 passed
- Lint/types: `uv run ruff check .` + `uv run pyright` → clean (0 errors/warnings)

**Completion criteria:** (1) checkbox persists via PATCH 200 → "hidden on" tag + GET round-trips `include_hidden: true`; failure path reverts box + `role="alert"` canned message ✓; (2) flag OFF byte-identical (only `visible.md` indexed), ON indexes `.hidden/note.md` into the KB catalog, `EXCLUDED_DIRS` excluded both states ✓; (3) A2: flag OFF → `detail.pruned==1`, doc gone from catalog ✓; (4) PATCH bool-only/list-only/both/neither no-op, phase-89 fixed 422s unchanged, 404, anonymous 403 (incl. bool-only body) ✓; (5) env-fallback rows render no checkbox, WCAG-clean (aria-label, keyboard focus, visible label, text tag) ✓; (6) full gate green ✓; (7) commit left to the harness per instructions (no `git add`/`commit` run; phase files untouched).

**Deviations:** none — no defects found; no code changes were needed on this pass.

**Next pending phase:** `.agents/phases/todo/98_sync_summary_visibility`.

app/api/sync.py

@@ -36,7 +36,9 @@ decisions):
 4. ``import_sources(..., prune=True)`` over the single combined list
    (git checkouts + local dirs), honoring each row's ``ignore_paths``
    (phase 89 — the per-root ignore map is built in the same per-row
-   loop as the source list) — prune so files deleted upstream, out of
+   loop as the source list) and its ``include_hidden`` flag (phase 105
+   — the per-root hidden-folders map, same per-row construction) —
+   prune so files deleted upstream, out of
    a local dir, or newly matching an ignore pattern leave the index
    (pruning covers the union; the CLI's no-prune default is unchanged);
 5. when the import changed the KB (added + updated > 0),
@@ -231,6 +233,7 @@ async def _run_sync() -> None:
         sources_root = Path(settings.sources_dir).expanduser()
         sources: list[Path] = []
         ignore_by_root: dict[str, list[str]] = {}
+        include_hidden_by_root: dict[str, bool] = {}
         for row in rows:
             if row.kind == "git":
                 root = clone_or_pull(row.url, sources_root / repo_name(row.url))
@@ -250,6 +253,14 @@ async def _run_sync() -> None:
             # edge.
             if row.ignore_paths:
                 ignore_by_root.setdefault(str(root), []).extend(row.ignore_paths)
+            # Phase 105 (A1/A4): the row's hidden-folders flag, keyed by
+            # the SAME root string the importer sees; a shared-root
+            # collision ORs — if EITHER row says "index hidden", the
+            # root does (the ignore-map union's boolean mirror).
+            include_hidden_by_root[str(root)] = (
+                include_hidden_by_root.get(str(root), False)
+                or bool(row.include_hidden)
+            )
         # Phase 64 (task 02): the per-file progress hook — the status
         # endpoint reports the file being processed right now. The
         # closure captures the module ``_status`` exactly like the state
@@ -260,7 +271,8 @@ async def _run_sync() -> None:
             _status.files_total = total
 
         summary: ImportSummary = await import_sources(
-            sources, llm, prune=True, progress=_hook, ignore_by_root=ignore_by_root
+            sources, llm, prune=True, progress=_hook, ignore_by_root=ignore_by_root,
+            include_hidden_by_root=include_hidden_by_root,
         )
         overview = False
         if summary.added + summary.updated > 0: