chore: remove Python rune-mcp tree (v0.3 implementation)

The Go rune-mcp at internal/* + cmd/rune-mcp/ has reached parity (PR
#102 + #110 + #117) and end-to-end verification (#118, #122, #124),
which means the Python tree is now dead weight. Carrying both
implementations is actively misleading: a fresh contributor following
the in-repo install instructions would still land in mcp/ + agents/
and try to set up a venv that no longer ships, and parity audits keep
re-discovering the Python source instead of treating the Go side as
the source of truth.

Removed
-------

  agents/common/        12 files  (config, embedding, llm, schemas)
  agents/retriever/      4 files  (query_processor, searcher, synthesizer)
  agents/scribe/        12 files  (detector, llm_extractor, handlers, server)
  agents/tests/         16 files  (pytest suite)
  agents/__init__.py
  agents/README.md            (Python agents intro — gone with the impl)
  agents/SLACK_SETUP.md       (Slack notifier setup for Python scribe)
  mcp/                  18 files  (Python adapter + server + tests)
  requirements.txt            (root Python dependency list)
  scripts/migrate_embeddings.py (one-off Python migration helper)

  Total: 67 files, 17,815 lines.

Kept (intentional)
------------------

  agents/claude/{scribe,retriever}.md   referenced by .claude-plugin/
                                        plugin.json — agent prompts that
                                        the runtime loads
  agents/codex/scribe.md                Codex-side agent prompt
  agents/gemini/{scribe,retriever}.md   Gemini-side agent prompts
  benchmark/                            deferred (separate decision —
                                        rewrite in Go vs delete entirely)
  docs/v04/spec/python-mapping.md       parity blueprint that maps Python
                                        source to Go destinations; useful
                                        as a historical record post-deletion
  docs/migration/*.md                   migration plan + audit trail —
                                        intentional history
  scripts/bootstrap-mcp.sh and other    referenced by gemini-extension.json;
    Python-era shell scripts            removal blocked on Gemini support
                                        decision (separate PR)

Not in scope
------------

  .github/workflows/pr-tests.yml + pr-comment.yml — Python pytest CI;
    handled by PR #125 (ci-drop-python).
  README.md, CLAUDE.md, SKILL.md, AGENT_INTEGRATION.md, GEMINI.md,
    CONTRIBUTING.md — top-level docs still describe the v0.3 install
    flow; rewrite scheduled separately so this commit stays focused
    on code deletion.

Verification
------------

  go build ./...   passes
  go vet ./...     passes
  go test ./...    full suite passes (no test referenced deleted paths)
  grep across remaining .{go,md,json,sh,toml,yml,yaml} for the deleted
    paths returned zero hits — no dangling references.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: couragehong