feat: add native and automatic semantic updates

[nyldn]

Summary

• add graphify update <path> --semantic as one native incremental conductor for code, documents, communities, and reports
• route installed agent skills through that conductor instead of duplicating the semantic runbook
• add opt-in semantic_update=on_commit automation through the existing detached Git hook
• coalesce overlapping commits under the graph rebuild lock and retain failed or interrupted requests for automatic retry
• load only selected-backend credentials from an optional repo-relative env file; never source shell code or accept endpoint overrides from it
• preserve plain graphify update and unconfigured hooks as AST-only, no-LLM paths

Why

Mixed corpora repeatedly become partially stale because the native commands stop at different layers and the final semantic refresh depends on someone remembering a manual step. This PR makes the full refresh a reusable native operation, then lets each project explicitly opt into running it after commits.

The opt-in remains cost-visible and project-scoped: a backend is mandatory, .graphifyignore and persisted build settings are honored, code-only commits stay free, and no repository-provided command is executed.

Closes #1710.

Project configuration

# .graphifyrc
semantic_update=on_commit
semantic_backend=kimi
semantic_env_file=.env.local
# semantic_model=kimi-k2.6
# semantic_google_workspace=true

Verification

• focused hook, semantic-update, watcher, and skill-generation suite: 309 passed
• full suite excluding the pre-existing order-sensitive labeling assertion: 4,906 passed, 11 skipped, 1 deselected
• unfiltered full suite: 4,905 passed, 11 skipped, with only that unchanged thread-completion-order assertion failing
• uv run ruff check graphify/hooks.py tests/test_hooks.py tools/skillgen/gen.py
• uv run pyright graphify/hooks.py
• skill generation check, schema singleton, per-host coverage, monolith round-trip, and always-on round-trip all passed
• uv run graphify update . refreshed the project graph successfully