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Address the 4 open indexio/CLI bug reports filed today

Address the 4 open indexio/CLI bug reports filed today. Issue notes are at:

  1. docs/log/issue/issue-arash-20260328-192146-858687.md — indexio_build_status progress only updates between sources, not during
  2. docs/log/issue/issue-arash-20260328-193353-406929.md — projio CLI is completely silent, no output from any subcommand
  3. docs/log/issue/issue-arash-20260328-193406-431554.md — indexio status not available via MCP, corpus_list only shows aggregates
  4. docs/log/issue/issue-arash-20260328-193442-340432.md — indexio build needs a smart --update mode that builds only new/changed sources

Read each issue, then fix them:

For #1: In src/projio/mcp/rag.py, the _build_worker_script generates a Python snippet with _on_progress callback. Add a file-level progress counter that writes status every 30 seconds or every 50 files within a source, not just between sources.

For #2: Check src/projio/cli.py — likely missing argument parser setup, missing print statements, or main() not wired. Compare with the working indexio CLI entry point.

For #3: Add an indexio_status MCP tool in src/projio/mcp/rag.py that calls indexio status --json (subprocess, like build does) or reads the status manifest directly. Should return per-source stats (files, chars, chunks, last_built).

For #4: In src/projio/mcp/rag.py indexio_build() and in the indexio CLI build command, add logic: when no --sources specified and --update flag is set, read the status manifest, compare against configured sources, and only rebuild sources with no stats or where source files are newer than last build timestamp.

Run tests after each fix. Save and commit with a message per fix.

  • [[docs/log/issue/issue-arash-20260328-192146-858687.md]] — Issue #1 directly addressed in this task
  • [[docs/log/issue/issue-arash-20260328-193353-406929.md]] — Issue #2 directly addressed in this task
  • [[docs/log/issue/issue-arash-20260328-193406-431554.md]] — Issue #3 directly addressed in this task
  • [[docs/log/issue/issue-arash-20260328-193442-340432.md]] — Issue #4 directly addressed in this task
  • [[docs/log/issue/issue-arash-20260326-174001-720656.md]] — Related MCP tooling gap for indexio/RAG infrastructure