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README: semantic_query is not a tool, the tool count is 14 not 15, and the team artifact is not written by default #1297

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#2403
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README: semantic_query is not a tool, the tool count is 14 not 15, and the team artifact is not written by default#1297
#2403
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bugSomething isn't workingcypherCypher query language parser/executor bugsdocumentationImprovements or additions to documentationeditor/integrationEditor compatibility and CLI integrationparsing/qualityGraph extraction bugs, false positives, missing edgespriority/highNeeds near-term maintainer attention; high-impact bug, regression, safety issue, or release blocker.
Milestone
0.10.0-rc

Description

@melihemreguler
melihemreguler
opened on Jul 27, 2026

1. semantic_query is presented as a tool but is a parameter

The Search section introduces semantic_query as though it were an MCP tool. It is not:

cli semantic_query -> unknown tool: semantic_query

semantic_query exists only as a parameter of search_graph. The README's own MCP Tools table does not list it, so the two sections contradict each other.

2. Tool count is 14, not 15

The intro and the Manual MCP Configuration section both state 15 tools ("you should see codebase-memory-mcp with 15 tools"). The server advertises 14 via tools/list (paginated: 8 with nextCursor: 8, then 6).

3. The team-shared artifact is opt-in, not automatic

Team-Shared Graph Artifact says:

When you index, the artifact is written or refreshed

In practice persistence defaults to false (src/mcp/mcp.c:376), so index_repository reports artifact_present: false and no .codebase-memory/graph.db.zst is created unless persistence: true is passed explicitly.

4. The dead-code Cypher example is rejected by the engine

Supported Cypher offers WHERE NOT EXISTS { (f)<-[:CALLS]-() } as the dead-code example. The engine rejects the inbound form. See #1293.

Environment

  • Version: codebase-memory-mcp 0.9.0 (release binary, darwin-arm64)
  • OS: macOS 26.5.2, Apple Silicon
  • Repo under test: DeusData/codebase-memory-mcp @ af3ffbd

Activity

  1. github-actions
    added
    cypherCypher query language parser/executor bugs
    editor/integrationEditor compatibility and CLI integration
    parsing/qualityGraph extraction bugs, false positives, missing edges
    on Jul 27, 2026
  2. DeusData
    added
    bugSomething isn't working
    documentationImprovements or additions to documentation
    priority/normalStandard review queue; useful PR with ordinary maintainer urgency.
    on Jul 28, 2026
  3. DeusData
    added this to the 0.9.1-rc milestone on Jul 28, 2026

  4. DeusData commented on Jul 28, 2026

    @DeusData
    DeusData
    on Jul 28, 2026
    Owner

    Thanks for checking the README against the actual server rather than relying on the prose.

    The contradictions remain code-grounded on current main: semantic_query is a search_graph parameter in the tool schema (src/mcp/mcp.c:381-416), and persistence is explicitly default false (src/mcp/mcp.c:376). The server advertises the TOOLS array beginning at src/mcp/mcp.c:347, not a standalone semantic_query tool.

    PR #1315 is now linked to this documentation bug and is queued for review. I have routed the issue to 0.9.1-rc at priority/normal; that routing does not pre-approve the PR. Thank you for grouping the four concrete claims in one reproducible report.

  5. mindplay-dk commented on Aug 17, 2026

    @mindplay-dk
    mindplay-dk
    on Aug 17, 2026

    Also, the readme mentions trace_call_path, which is actually called trace_path.

    And there's an undocumented check_index_coverage tool as well.

    Maybe ask your agent to check if the documentation matches the codebase? 😊

  6. DeusData
    added
    priority/highNeeds near-term maintainer attention; high-impact bug, regression, safety issue, or release blocker.
    and removed
    priority/normalStandard review queue; useful PR with ordinary maintainer urgency.
    on Sep 5, 2026
  7. DeusData
    added a commit that references this issue on Sep 22, 2026

    docs: MCP tool count is 17; document the three missing tools

    58c1c0c
  8. daidaiJ
    added 2 commits that reference this issue on Sep 29, 2026

    docs: MCP tool count is 17; document the three missing tools

    6168467

    docs: MCP tool count is 17; document the three missing tools

    bcfd45d
  9. DeusData
    added a commit that references this issue on Sep 30, 2026

    Merge pull request #2403 from DeusData/fix/issue-1297

    39da5de
  10. DeusData
    closed this as completedin #2403on Sep 30, 2026
  11. TFSebben
    added a commit that references this issue on Sep 30, 2026

    docs(readme): semantic_query is a search_graph parameter; team artifa…

    95eaf01

  12. DeusData commented on Sep 30, 2026

    @DeusData
    DeusData
    on Sep 30, 2026
    Owner

    Thank you again for reporting this, @melihemreguler! The fix is now on main in 39da5de (merged via #2403), and it will ship in the next release.

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