Feat/component level updater - #111
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Replace file-level cache invalidation with a component-level updater: diff the saved dependency graph against the new one (body hash, signature, edges, rename pairing), repair the module tree (renames, deletions, routing rules 1-3, routing agent for orphans, growth check), build a per-leaf change report (Own / Up / RefCh / Tree), check the fallback ratios, then run one editing agent per active leaf, in dependency order, restricted to a write set enforced by str_replace_editor. Missing pages are regenerated by the normal pipeline, a stale-name scan fixes leftovers, and every decision, verdict and call cost lands in update_record.json. `codewiki generate --update` now runs the new updater (rung 3); `--update-rung 0` keeps the previous file-level behaviour as the baseline, rungs 1/2/3b are ablations, and --tau-*/--k-hop/ --max-diff-tokens override the hyperparameters. Also: LLMBackend.run_update_agent + last_usage on both backends, allowed_write_paths on CodeWikiDeps, absolute/.. path rejection in the pydantic-ai editor path, and a guard on the module-level stdout rewrap in str_replace_editor that broke pytest capture.
… files The dependency graph is named after the checkout directory. With one worktree per revision, each update left a new *_dependency_graph.json next to the older ones, and snapshot_old_graph refused to choose among several, so the update fell back to a full build with 'previous dependency graph not found'. - find_any_graph_file: several candidates resolve to the newest (logged) - prune_superseded_graphs: after a successful update, drop graph files other than the current checkout's, so the next update finds one - tests for both paths
Move the module-level logger definition below the import block so all imports sit at the top of the file. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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