fix: prevent stale CodeGraph data from appearing current

[FaithZL]

Summary

• attempt one bounded incremental CodeGraph sync before every identity-safe proxy query, including clean-HEAD status windows
• preserve unknown pre-query evidence, downgrade failed syncs to navigation-only stale context, and publish source_of_truth: false
• introduce runtime bundle v3 while retaining bundle v1/v2 read compatibility
• advance Polaris to 0.1.23 with a version-only migration; Workflow remains 0.1.3
• document and test clean committed changes and clean branch switches with the real CodeGraph CLI

Verification

• python3 tests/run_tests.py (237/237 passed)
• python3 -m compileall -q polaris_cli.py scripts tests
• python3 scripts/check_docs.py --help
• git diff --check

Compatibility

• runtime remains Python-standard-library-only
• no daemon, watcher, retry loop, full codegraph index, or workflow-version change
• durable Code Intelligence record v3 is unchanged; historical bundle v1/v2 remain readable