phase: 89_source_ignore_paths

All verification complete — TODO.md was already cleared in the roadmap commit; the two extra unit-test diffs are necessary fake-signature adaptations for the new keywords. Everything is green, no fixes were needed.

## Phase 89 — final verification pass: ALL GREEN

**Verified (all 6 task files present in `complete/`):**
- `git_sources.ignore_paths` JSONB column + migration 0013; `alembic downgrade -1 && upgrade head` round-trips (head `0013`)
- Importer: `normalize_ignore_path`/`is_ignored`/`_ignore_for_root`, `ignore` in walk + progress pre-walk, `ignore_by_root` in `import_sources`
- API: GET/POST carry list; admin-only `PATCH` (replace, 404/422 fixed details, anonymous 403)
- Pipelines wired: `_run_sync`, `_run_upload` re-upload, `scripts/import_docs.py`
- Sources-page box: dialog, §7.4 save lifecycle, `N ignored` tag, a11y; env rows get no box

**Test/lint results:**
- `uv run pytest` → 1808 passed
- `uv run pytest --cov=app --cov-report=term-missing` → TOTAL **99%** (>90%)
- `uv run pytest tests/e2e/test_source_ignore_paths.py -v --no-cov` → 6 passed (isolated, DB up)
- Regressions in isolation: `test_git_sources_admin` 6, `test_archive_upload_sources` 5, `test_sync_button` 3, `test_smoke` 3 — all passed
- `uv run ruff check . && uv run pyright` → clean (0 errors)

**Completion criteria:** box→PATCH 200→count+GET round-trip ✅ · sync excludes `ignore/` (no docs/chunks/embeddings/summaries) + prunes newly-ignored (pruned==2) ✅ · no-mid-path rule E2E ✅ · PATCH 404/422/replace/clear/403 ✅ · full gate green ✅ · commit + phase move left to harness per rules.

**Deviations:** none blocking — E2E pins `files == 4` (overview's "5" was an off-by-one vs its own 6-file tree, documented in-test); `tests/unit/test_importer.py` + `test_sync_button.py` test-double fakes extended for the new keywords (needed for the suite to stay green).

**Next pending phase:** none — `todo/` holds only this phase.

tests/integration/test_git_sources_upload.py

@@ -291,6 +291,7 @@ class _GatedImport:
         limit: int | None = None,
         session: object = None,
         progress: Callable[[str, str, int, int], None] | None = None,
+        ignore_by_root: dict[str, list[str]] | None = None,  # phase 89
     ) -> ImportSummary:
         self.prune_flags.append(prune)
         if progress is not None:
@@ -1352,3 +1353,92 @@ def test_models_down_fails_the_run_and_leaves_folder_and_row(
     # The scan never ran: no docs, no stray temps.
     assert _docs(upload_client) == []
     assert [p.name for p in uploads.iterdir()] == ["homelab"]
+
+
+# --- phase 89: re-uploads honor the row's saved ignore list -------------------
+
+
+def test_reupload_honors_saved_ignore_list(
+    upload_client: TestClient, monkeypatch: pytest.MonkeyPatch, db: Session, tmp_path: Path
+) -> None:
+    """Phase 89: a re-upload of an EXISTING source honors the ignore
+    list saved on its row. First scan (fresh row, no list) indexes the
+    ignored file too; once the list is saved via the API, re-uploading
+    the same archive again scans only the kept file — the previously
+    indexed ignored file leaves the KB (prune), and the run lands
+    ``success`` with counts that exclude it. The upload itself keeps
+    every file on disk: the ignore is about the index, not the folder."""
+    uploads = tmp_path / "uploads"
+    _point_at(monkeypatch, uploads)
+    _real_llm(monkeypatch)
+    files = {
+        "keep.md": "# Keep\nin scope\n",
+        "ignore/secret.md": "# Secret\nignored\n",
+    }
+    r = _post(upload_client, "docs.tar.gz", _targz_bytes(files))
+    assert r.status_code == 202, r.text
+    status = _wait_status(upload_client)
+    assert status["state"] == "success", status
+    # First scan: the fresh row has no list → both files are indexed.
+    assert status["detail"]["files"] == 2
+    assert _docs(upload_client) == [("docs", "ignore/secret.md"), ("docs", "keep.md")]
+
+    # Save the ignore list on the row via the API (phase 89, task 03).
+    folder = uploads / "docs"
+    row = _row(db, str(folder))
+    assert row is not None
+    r = upload_client.patch(
+        f"/api/git-sources/{row.id}", json={"ignore_paths": ["ignore/"]}
+    )
+    assert r.status_code == 200, r.text
+    assert r.json()["ignore_paths"] == ["ignore"]  # stored normalized
+
+    # Re-upload the SAME archive (same name → in-place replace).
+    r = _post(upload_client, "docs.tar.gz", _targz_bytes(files))
+    assert r.status_code == 202, r.text
+    status = _wait_status(upload_client)
+    assert status["state"] == "success", status
+    detail = status["detail"]
+    # The scan walked only keep.md (unchanged); the ignored file never
+    # entered the walk, so prune dropped the first scan's row for it.
+    assert detail["files"] == 1
+    assert detail["added"] == 0
+    assert detail["updated"] == 0
+    assert detail["unchanged"] == 1
+    assert detail["pruned"] == 1
+    assert _docs(upload_client) == [("docs", "keep.md")]
+
+    # The re-upload left the row's list in place (the existing row is
+    # untouched by the upsert), and the folder keeps every file.
+    row_after = _row(db, str(folder))
+    assert row_after is not None
+    assert row_after.ignore_paths == ["ignore"]
+    assert {p.name for p in folder.iterdir()} == {"keep.md", "ignore"}
+
+
+def test_upload_new_source_without_list_imports_everything(
+    upload_client: TestClient, monkeypatch: pytest.MonkeyPatch, db: Session, tmp_path: Path
+) -> None:
+    """Phase 89 regression: an upload of a NEW source name (no row yet,
+    hence no ignore list) imports everything in the archive — including
+    nested files — exactly as before phase 89."""
+    uploads = tmp_path / "uploads"
+    _point_at(monkeypatch, uploads)
+    _real_llm(monkeypatch)
+    files = {
+        "alpha.md": "# Alpha\nroot file\n",
+        "sub/deep.md": "# Deep\nnested file\n",
+    }
+    r = _post(upload_client, "fresh.tar.gz", _targz_bytes(files))
+    assert r.status_code == 202, r.text
+    status = _wait_status(upload_client)
+    assert status["state"] == "success", status
+    detail = status["detail"]
+    assert detail["files"] == 2
+    assert detail["added"] == 2
+    # The fresh row carries the server-default empty list: nothing was
+    # ignored.
+    row = _row(db, str(uploads / "fresh"))
+    assert row is not None
+    assert (row.ignore_paths or []) == []
+    assert _docs(upload_client) == [("fresh", "alpha.md"), ("fresh", "sub/deep.md")]