Address the 4 open indexio/CLI bug reports filed today¶

Goal¶

(promoted from note)

Context¶

(see source note)

Prompt¶

Fix the issue described in /storage2/arash/projects/projio/docs/log/issue/issue-arash-20260328-193731-044867.md. Read it first, then implement the proposed fix.

Acceptance Criteria¶

[ ]

Result¶

Completed in 367.4s (1 steps, model: opus)

Session: 0ed4146e-eb76-40cc-8225-34172319c225 Result note: /storage2/arash/worklog/workflow/captures/20260328-195054-7d1a1d/note.md

Output¶

Here's a summary of all 4 fixes:

**Fix #1** (`rag.py:_build_worker_script`): Added a `threading.Timer`-based periodic updater that writes progress every 30 seconds during long source builds. Previously, progress only updated between sources — now the status file is refreshed continuously even within a single large source.

**Fix #2** (`cli.py`): Added `if __name__ == "__main__": main()` at the end of `cli.py`. This makes `python -m projio.cli` work (previously it was silent because the module defined `main()` but never called it when executed directly).

**Fix #3** (`rag.py:indexio_status`, `server.py`): Added a new `indexio_status()` MCP tool that returns per-source stats with change detection. Each source shows its state (`indexed`, `changed`, `not_yet_built`, `missing_files`, `empty_match`), file/char/chunk counts, and the response includes `actionable_source_ids` for sources needing rebuild.

**Fix #4** (`rag.py:indexio_build`, `server.py`): Added `update=True` mode to `indexio_build`. When set (and no explicit `sources` list), it reads the status manifest, compares file states via `source_snapshot()`, and only rebuilds sources that are new or changed. Returns `"status": "up_to_date"` if nothing needs building.

Tests: 70 passed, 1 pre-existing unrelated failure.

## Next Steps

1. Commit these changes with `datalad_save` and update the 4 issue notes to `status: done`.
2. Update the MCP tool routing instructions in CLAUDE.md, worklog CLAUDE.md, and projio codegen to document the new `indexio_status` tool and `update` parameter.
3. Add the `--update` flag to the indexio CLI `build` subcommand in `packages/indexio/src/indexio/cli.py` so it's available from the command line too.