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[Bug] Managed skill directs issue audits to a removed MCP tool #292

Description

@morluto

Description

The managed Codex skill tells agents to start exact issue audits with workflow.prepare_issue_set or corpus.get_coverage, but the unified MCP catalog deliberately filters workflow.prepare_issue_set out through removedCompositeTools.

This leaves a dead tool route in the generated guidance. An agent following the preferred exact-audit path gets a tool-not-found result and must infer a different composition from lower-level acquisition and corpus operations. The fallback named in the sentence, corpus.get_coverage, reports coverage but is not itself an exact issue audit.

This is distinct from #194 and #195. Those issues concerned capabilities hidden behind optional toolsets and were closed when the product moved to one unified catalog. Here, the generated guidance and that unified catalog disagree.

Steps to Reproduce

  1. Install or inspect GitContribute v3.0.0 and run the managed Codex setup.
  2. Read the generated skill in internal/setup/setup.go; its issue workflow names workflow.prepare_issue_set as the first exact-audit entrypoint.
  3. List the MCP tools from the unified server.
  4. Observe that workflow.prepare_issue_set is absent because internal/mcpserver/catalog.go includes ToolPrepareIssueSet in removedCompositeTools.

The same mismatch is present on current main.

Expected Behavior

Managed workflow guidance should name only advertised operations and describe the supported facts-first sequence for exact issue audits, including the recovery path when coverage is incomplete.

A regression test should compare tool names referenced by managed guidance with the advertised catalog, or otherwise prevent removed tools from remaining canonical skill entrypoints.

Actual Behavior

The skill advertises workflow.prepare_issue_set, while the server intentionally omits it from tools/list. The released v3.0.0 source contains both the stale instruction and the removal map.

Environment

  • OS: Linux 7.0.0-29-generic
  • Go version: go version go1.26.5 linux/amd64
  • GitContribute version: v3.0.0 source tag (74c8da3); also reproduced by source inspection on current main (832c7f4)

Additional Context

workflow.prepare_issue_set was introduced for exact issue evidence in commit ee1f97c. The managed skill added it as an entrypoint in 4f825649. Commit 32043b4 later established the breaking facts-first catalog boundary and removed the composite from advertisement without updating the skill.

The live github.search_threads primitive correctly found the related upstream PR in the investigation that exposed this mismatch and marked repository-wide coverage as incomplete. That behavior is working as intended; this report is specifically about stale managed routing guidance.

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