fix(hooks,flows): prevent duplicate hooks on reinstall and resolve relative vs absolute path mismatch (#558, #569, #576)

[Blazehue]

Resolves #558, #569, #576

Summary of Fixes

• [Bug]: claude-code hooks in settings.json shall not contain absolute paths to the repo #558: Updated _merge_hooks_into_settings in code_review_graph/skills.py to update existing code-review-graph hooks in-place, preventing duplicate hook entries when re-running code-review-graph install. Added regression test test_install_hooks_reinstall_does_not_duplicate.
• Incremental flow re-detection never finds new entry points (relative vs absolute path mismatch) #569: Resolved relative vs. absolute path mismatch in incremental_trace_flows (code_review_graph/flows.py). Expanded changed_files to match both relative and absolute representations in SQL queries and entry point filtering (_matches_changed_files). Added regression test test_incremental_trace_flows_relative_vs_absolute_path_mismatch.
• CALLS edges are emitted for calls inside statically-dead code (if False:, if TYPE_CHECKING:, #if 0) #576: Verified dead-code reachability guards (if False:, if TYPE_CHECKING:, #if 0, if (false)) so calls in statically dead branches produce no CALLS edges.

Verification

• Full test suite: 2,398 passed, 0 failures in pytest.