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decision(mcp-runtime): guard the call sites in a shared helper instead of making runCli restore the level itself - the CLI process exits right after that call, so the mutation is only ever a problem for the long-lived MCP server, and cliRun.ts keeps its current single-writer behaviour for the CLI and library callers. constraint(logger): runCli repoints the module-level logger singleton for every quiet/stdout pack and never puts it back, so one generate_skill call silenced logger.error for the remainder of the session. learned(mcp-runtime): packCodebaseTool had already worked around this locally and documented why; the two sibling packing tools carried no such guard. Routing all three through the wrapper makes the invariant hold for tools added later.
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Included review availability: Your plan provides up to 10 included reviews per hour; 9 remain after this review. 📝 WalkthroughWalkthroughThe MCP runtime adds a shared wrapper that preserves the logger level across successful, failed, and overlapping CLI executions. Skill generation and repository packing use the wrapper. Tests cover restoration, concurrency, error propagation, result passthrough, and argument forwarding. ChangesMCP log-level preservation
Priority: ➖ Normal Estimated code review effort: 3 (Moderate) | ~20 minutes Change: Bug fix · Severity of issue fixed: Medium Sequence Diagram(s)sequenceDiagram
participant MCPTool
participant runCliPreservingLogLevel
participant runCli
participant logger
MCPTool->>runCliPreservingLogLevel: start CLI pack
runCliPreservingLogLevel->>logger: save initial level
runCliPreservingLogLevel->>runCli: execute pack
runCli->>logger: set CLI log level
runCli-->>runCliPreservingLogLevel: complete or fail
runCliPreservingLogLevel->>logger: restore level after final active pack
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In `@src/mcp/tools/mcpToolRuntime.ts`:
- Line 182: Update runCliPreservingLogLevel around the shared logger override to
prevent overlapping MCP packing calls from reading, changing, or restoring stale
global log levels. Serialize the critical section across the logger-level
capture, runCli execution, and restoration, while preserving the existing
log-level behavior.
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decision(mcp-runtime): refcount the in-flight packs instead of serializing them. The MCP SDK starts each tool handler without waiting for the previous one, so a per-call save/restore let a second quiet pack save the SILENT level the first one had just installed and hand that back on exit, which re-blinds the session the previous commit set out to fix. A counter closes the hole without taking away the parallelism packs already have. constraint(logger): the log level is process-global, so while any pack is running the level has to stay as quiet as that pack asked for; the saved value is the one from before the first pack in the current group. learned(mcp-runtime): the interleaving is deterministic, not a heisenbug - runCli lowers the level before its first await, so the second call always observes the value the first one wrote. Reproduced over real stdio with two concurrent generate_skill calls, and the new unit test fails against the per-call restore.
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Update after the automated review ( The first commit saved and restored the level per call, which is not enough. The MCP SDK starts each tool handler without waiting for the previous one, and
Measured over real stdio (two
Regression test: |
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Closes #1864
Summary
runCli()repoints the shared module-level logger singleton forquiet/stdoutruns and neverrestores it. That is fine for the CLI — the process exits — but the MCP server is long-lived, so a
single
generate_skillorpack_remote_repositorycall leaveslogger.error()dead on stderr forthe rest of the session (#1864).
packCodebaseToolhad already documented the hazard and worked around it locally. This PR liftsthat workaround into
src/mcp/tools/mcpToolRuntime.tsasrunCliPreservingLogLevel()and routesall three packing tools through it, so the invariant the repo already states is now enforced for the
two tools that were missing it, and for any quiet tool added later.
Changes
src/mcp/tools/mcpToolRuntime.ts— addrunCliPreservingLogLevel(directories, cwd, options):save
logger.getLogLevel()before the first in-flight pack,await runCli(...), and restore infinallyonly when the last one finishes. The refcount matters: the MCP SDK starts each toolhandler without waiting for the previous one, so a per-call restore would have the second quiet
pack save the SILENT level the first installed and hand that back (raised this in review on
8fc4c21fby @coderabbitai).src/mcp/tools/generateSkillTool.ts,src/mcp/tools/packRemoteRepositoryTool.ts— call thewrapper instead of
runClidirectly.src/mcp/tools/packCodebaseTool.ts— call the wrapper; its inline save/restore (and therunCli/loggerimports it needed) goes away, comment kept short and pointing at the helper.tests/mcp/tools/mcpToolRuntime.test.ts— 4 unit tests: level restored after a quiet pack, levelrestored when the pack throws, CLI result passed through unchanged, arguments forwarded verbatim.
Evidence
The repro script from #1864, run against a built checkout (
node repro.mjs <repo> <fixture>):generate_skillgenerate_skillmain@9f01703a(1.18.0)8fc4c21f(per-call restore)e40c4ccb(this branch)All rows are the same scripts, same fixture, same Node, rebuilt from each commit. The middle row is
what the review above is about; the third column drives two packs without awaiting the first.
Also verified locally:
vitest run(full suite, non-watch) — 1825 passed, 20 skipped, 1 file skipped, 0 failures.8fc4c21f's wrapper it fails withexpected 3 to be -1, so it does pin the race rather than pass by construction.npm run lint— biome clean (the 431 files it touched were line-ending-only,git diffon them isempty), oxlint 0 warnings / 0 errors,
tsc --noEmitclean, secretlint clean.packCodebaseTool/packRemoteRepositoryTooltests still assert onrunClidirectly and keep passing: their
vi.mock('.../mcpToolRuntime.js')factories spread...actual,so the real wrapper runs and still reaches the mocked CLI.
Scope
runCli()itself, to CLI output, or to what the tools return to the agent. The packstays quiet while it is running; only the level it leaves behind is restored, so nothing new is
written to the stdio channel the agent reads.
tool contract is unchanged.
--verboseMCPserver keeps DEBUG across a pack.
Checklist
npm run testnpm run lintReproduced, measured and written by me with an AI coding agent (Qoder) assisting; happy to answer
follow-ups.