chore: remove Python rune-mcp tree (v0.3 implementation) - #129
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couragehong merged 1 commit intoMay 8, 2026
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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>
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The six top-level docs still described the v0.3 install flow — a Python
venv prepared by scripts/bootstrap-mcp.sh, mcp/server/server.py spawned
under .venv/bin/python3, agents/{common,scribe,retriever}/ as the
business-logic packages, etc. After PR CryptoLabInc#129 (remove-python-tree) all of
that is gone, but a contributor following these docs would still try to
set it up and land in a dead end.
This rewrite anchors every doc on the v0.4 truth: a single Go binary
(cmd/rune-mcp) that the host CLI auto-spawns over stdio, runtime
preparation done at install time, runtime health visible through the
diagnostics + vault_status MCP tools.
Per file
--------
README.md (small)
- drop the dead `scripts/check-infrastructure.sh` reference
- point Related Projects at envector-go-sdk (the Go FHE SDK we
actually depend on now) instead of pyenvector
CLAUDE.md (one-line)
- "Writing Python scripts to /tmp" → "Writing scripts to /tmp" in the
routing table NOT-do column (the rule still holds; the Python
qualifier was v0.3-specific)
GEMINI.md (medium)
- replace the Plugin Root Detection / Runtime Preparation block,
which mandated SETUP_ONLY=1 scripts/bootstrap-mcp.sh and
.venv/bin/python3 sanitization, with v0.4 guidance: the binary is
auto-spawned, health is observable via diagnostics, no venv exists
SKILL.md (medium-large)
- Execution Model: drop scripts/bootstrap-mcp.sh as the
"single source of truth" — the binary itself is now the runtime
- Activation Check: drop the Local Runtime Check (step 0) that
required the bootstrap script; drop the envector.endpoint /
envector.api_key field requirement (those come via Vault bundle now)
- /rune:configure: drop scripts/check-infrastructure.sh validation
step; replace with reload_pipelines + diagnostics rendering
- /rune:status: drop "Python venv" / "MCP servers running" rows;
render diagnostics' per-subsystem snapshot instead
- /rune:activate: drop the "check Python environment" step
- /rune:reset: drop "stop MCP servers" — the host CLI manages process
lifecycle, the user does not
AGENT_INTEGRATION.md (full rewrite, 278 lines → equivalent shape)
- drop all .venv/bin/python3 + mcp/server/server.py invocations
across Claude / Codex / Gemini / OpenAI sections
- replace install.sh / install-codex.sh / ensure-codex-ready.sh
references with plugin/skill/extension install commands
- rewrite the OpenAI integration around stdio against the Go binary
(the agents-sdk + Responses API patterns just point command= at
bin/rune-mcp)
- acknowledge that gemini-extension.json still calls bootstrap-mcp.sh
as a known follow-up under the Gemini track (not in this PR's
scope to resolve)
CONTRIBUTING.md (medium)
- Prerequisites: Python 3.12 → Go 1.26.2+ (toolchain pinned in go.mod)
- test instructions: pytest agents/tests/ → go test -race ./...
- Cross-Agent Invariant Checklist: replace bootstrap-mcp.sh items
with "Go binary is single MCP entry point" / manifest consistency
- Project Structure: redraw the tree against current layout
(cmd/rune-mcp, internal/{mcp,service,lifecycle,adapters,domain,
policy,obs}, agents/{claude,codex,gemini}/*.md only, scripts/dev/
v04/, etc.) — the old tree showed mcp/server/server.py and
agents/common/ that no longer exist
- Release Process: bump example version 0.2.0 → 0.4.0; tests command
updated; reference Task CryptoLabInc#30 for the binary distribution pipeline
Out of scope
------------
- gemini-extension.json bootstrap-mcp.sh path (Gemini track)
- scripts/ Python-era shell scripts cleanup (Gemini track)
- examples/ patterns/ setup/ config/ docs (separate A4 pass)
- package.json + .claude-plugin/plugin.json version bump (separate A5)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
heeyeon01
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Jul 7, 2026
The Python pytest pipeline at .github/workflows/pr-tests.yml currently fires on every PR open / synchronize / reopen, regardless of base branch. Across the v0.4 Go migration line that's pure noise: every PR into feat/go-migration runs the v0.3 pytest suite against a working tree where the Python source is being deleted out from under it (Python tree removal already landed via PR CryptoLabInc#129). The runs all fail or no-op, which trains contributors to ignore CI status — the worst possible state to be in when CI matters again at main-merge time. Narrow the trigger so the workflow only fires when the PR's base branch is `main`. That preserves the workflow scaffolding for the final feat/go-migration → main integration moment, when CI itself will be rewritten as Go (build / vet / fmt / test -race) so it actually exercises the v0.4 code at the boundary. Effect on PR streams -------------------- PR base = feat/go-migration → no CI run (silent) PR base = main → CI runs (existing pytest pipeline, to be rewritten at main-merge) pr-comment.yml is unchanged — it chains off `workflow_run: workflows: ["PR Tests"]`, so when pr-tests stays quiet, pr-comment stays quiet too. No edit needed there. Side effects ------------ - PR CryptoLabInc#125 (ci-drop-python) currently sits open and proposes a Go CI rewrite. With this gate in place there is no CI noise to fight, so CryptoLabInc#125's urgency drops. The cleanest path is to close it and redo the Go CI as part of the main-merge integration PR — that way the CI lands together with whatever the boundary actually needs (artifact uploads, GOPRIVATE auth, OS matrix, etc.) rather than having two CI rewrites land independently. - .github/workflows/pr-tests.yml still references .github/scripts/ci_changed_tests.py and requirements.txt, both of which exist in main but not on feat/go-migration after PR CryptoLabInc#129. That is intentional — the workflow scaffolding stays bound to main's contents, and the rewrite at main-merge time will replace both anyway. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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The Go rune-mcp at
internal/*+cmd/rune-mcp/has reached parity and end-to-end verification, 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/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__.pyagents/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}.mdagents/codex/scribe.mdagents/gemini/{scribe,retriever}.mdbenchmark/docs/v04/spec/python-mapping.mddocs/migration/*.mdscripts/bootstrap-mcp.shand other referenced bygemini-extension.json;Python-era shell scriptsremoval blocked on Gemini support decision (separate PR)Not in scope