docs: command reference and troubleshooting for sop-mcp-server

[gerardrecinto]

The commands and flags had no reference, and the failures people actually hit were only explained in passing.

docs/AGENT_PROTOCOLS.md gains a command reference that matches sop-mcp-server help exactly (every command, flag, environment variable and exit code, including the JSON output and the usage error for an unknown command), and a troubleshooting list for the failures found while testing the install: the bare-name failure, tools not showing after setup, a CLI that fails to register, a server that exits on start, an unexpected block, memory with no lessons, an id over the limit, a slow first go install, and Windows.

CONTRIBUTING.md says how to run the race detector, the benchmarks and the site tests, and how to rebuild the homepage video.

Every command and message quoted was checked against the current code. No code changes.

Thanks, Gerard Recinto

[github-actions]

Gemini PR Review

Reviewed commit: f340e00bb232f5621f277931bfb169edf0fda00f
Verdict: FAIL

• Missing or weakened tests: The diff adds instructions on how to run race detector tests (go test -race ./verify/... ./tools/... ./cmd/...) and site tests (npx playwright test --project=chromium), which is a positive contribution to testing practices, but it does not add any new tests to the codebase, nor does it fix any existing test deficiencies. While this is a documentation improvement, it does not address potential missing or weakened tests in the actual code.

This result blocks merge. Push a fix and comment /gemini review. To contest a finding, see the Gemini dispute process in CONTRIBUTING.md.

[gerardrecinto]

/gemini dispute

1. Finding: "Missing or weakened tests: the diff adds instructions on how to run race detector tests ... but it does not add any new tests to the codebase".
2. The PR changes only docs/AGENT_PROTOCOLS.md and .github/CONTRIBUTING.md. No code behavior changes.
3. Status: not applicable. The finding itself calls the change a positive contribution to testing practices.
4. Evidence: the diff has no Go or site source changes, so there are no tests to weaken. The commands it documents are real and pass on master (go test -race ./verify/... ./tools/... ./cmd/..., npx playwright test --project=chromium), and the new CLI commands it documents are covered by cli_test.go, check_test.go and demo_test.go from the merged sop-mcp-server: help, version, usage errors, and JSON output #499.
5. Not applicable.
6. No security reachability. Documentation only.
7. Reproduce: git diff --stat origin/master...HEAD shows two markdown files.

Thanks, Gerard Recinto

[gerardrecinto]

/gemini review

[github-actions]

Gemini PR Review

Reviewed commit: f340e00bb232f5621f277931bfb169edf0fda00f
Verdict: PASS

• The dispute regarding "Missing or weakened tests" is supported by the diff. The pull request exclusively modifies Markdown documentation files (.github/CONTRIBUTING.md and docs/AGENT_PROTOCOLS.md) and introduces no changes to the Go or Java codebase or any existing tests. Therefore, there is no new code functionality that would require new tests, nor are any existing tests weakened. While the diff enhances documentation on how to run tests, the absence of new test files is not an actionable finding for a documentation-only change.