[codex] Update skills for Tool API v3

[rodion-m]

Summary

• Updates CodeAlive skill scripts to call Tool API v3 /api/tools/{name} endpoints.
• Defaults CLI output to agentic format where appropriate and adds repository/artifact query commands.
• Refreshes README/SKILL guidance for the v3 tool contract.

Cross-repo rollout

• Depends on backend Tool API v3 PR and aligns with codealive-mcp v3 tool names.
• Companion documentation PR publishes the updated setup instructions.

Verification

• Full skills test suite: 13 passed.
• Targeted checks: pytest tests/test_tool_api_v3.py tests/test_fetch_format.py: 13 passed.

[gemini-code-assist]

Code Review

This pull request updates the CodeAlive context engine skill to version 3.0.0, transitioning to the stateless Tool API v3. It introduces several new scripts (metadata.py, ontology.py, read_file.py, schema.py, tree.py) and refactors existing scripts and the shared api_client.py to route requests through the new tool method, defaulting to backend-rendered agentic output. The review feedback identifies a serialization bug in the api_client.py CLI, outdated documentation regarding identifier limits in fetch.py, dead code in fetch.py that can be cleaned up, and a lack of exception handling for integer parsing in read_file.py and tree.py.

Important

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[rodion-m]

Self-review pass completed.

Finding addressed before reviewer wait:

• The context explorer agent guidance still used codebase_consultant as an example trigger. I replaced it with canonical chat wording and pushed 85522fb.

Rechecked:

• No legacy alias strings remain in the repository.
• uv run pytest -q: 13 passed.
• Left unrelated untracked FRESHNESS_DESIGN.md out of the PR.

[rodion-m]

Review follow-up pushed in 52e35d3.

Addressed Gemini findings:

• datasources CLI now requests output_format="json" before JSON-printing.
• Updated fetch identifier limit docs from 20 to 50.
• Removed obsolete fetch formatter dead code and its obsolete formatter tests.
• Added graceful integer parsing errors for read_file.py and tree.py numeric options.
• API client now sends relationship profiles as canonical snake_case values.

Rechecked: uv run pytest -q: 7 passed.