[codex] Switch MCP tools to Tool API v3

[rodion-m]

Summary

• Switches MCP tools from legacy backend routes to Tool API v3 /api/tools/{name} calls.
• Registers the v3 canonical tool set and removes deprecated alias registration.
• Adds v3 wrapper coverage, metadata assertions, and documentation updates.

Cross-repo rollout

• Depends on backend Tool API v3 PR in CodeAlive-AI/backend.
• Companion PRs update codealive-skills and documentation.

Verification

• Full MCP test suite: 142 passed.
• Targeted v3 tests: pytest src/tests/test_tool_api_v3.py src/tests/test_tool_metadata.py: 14 passed.

[gemini-code-assist]

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[rodion-m]

Self-review pass completed.

Finding addressed before reviewer wait:

• Root-level smoke/integration scripts and CLAUDE.md still mentioned removed legacy aliases (codebase_search, codebase_consultant). I removed those references and pushed f1c422a.

Rechecked:

• MCP registered tools match the Tool API v3 canonical list exactly.
• No legacy alias strings remain in the repository.
• CI test path uv run pytest src/tests -q: 142 passed.
• Manual smoke/integration scripts compile with python -m py_compile smoke_test.py integration_test.py.

[rodion-m]

Review consistency follow-up pushed in 13c2521.

Changed MCP relationship profile payloads to the Tool API v3 canonical snake_case values (calls_only, inheritance_only, all_relevant, references_only). Backend remains tolerant of old Pascal/camel variants, but MCP now emits the public v3 contract.

Rechecked: uv run pytest src/tests -q: 142 passed.