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`.

alembic/versions/0019_git_source_include_hidden.py

@@ -0,0 +1,52 @@
+"""git_sources.include_hidden: per-source hidden-folders flag (phase 105)
+
+Revision ID: 0019
+Revises: 0018
+Create Date: 2026-09-12
+
+Phase 105 (per-source hidden-folders toggle: dot-prefixed paths become
+indexable per input — the owner flips a "Hidden" checkbox next to the
+"Ignore paths" button on the Sources page): when the flag is ON, the
+importer walk (``app.rag.importer.iter_importable_files``) no longer
+skips dot-prefixed path components for that source — files inside
+hidden folders AND hidden files with an importable extension are
+indexed, embedded, and summarized exactly like visible files (A1).
+``EXCLUDED_DIRS`` (``.venv``, ``node_modules``, ``.git``, …) stay
+excluded in BOTH states, and the extension filter always applies. The
+flag takes effect on the NEXT sync (no auto-sync — the ignore-list
+precedent, phase 89); a previously indexed hidden file is pruned on
+the next sync after the flag flips OFF (A2). One additive, fully
+reversible column (A13), no other schema change:
+
+* ``git_sources.include_hidden`` — BOOLEAN NOT NULL with server
+  default ``false``: every pre-phase-105 row reads ``False`` —
+  byte-identical import behavior until the owner flips it (A4).
+"""
+from __future__ import annotations
+
+import sqlalchemy as sa
+
+from alembic import op
+
+revision = "0019"
+down_revision = "0018"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "git_sources",
+        sa.Column(
+            "include_hidden",
+            sa.Boolean(),
+            server_default=sa.text("false"),
+            nullable=False,
+        ),
+    )
+
+
+def downgrade() -> None:
+    # The column is the only 0019 artefact — dropping it leaves
+    # 0018's schema byte-identical (A13, fully reversible).
+    op.drop_column("git_sources", "include_hidden")