- Removed `pi-natives` chunk language classifier modules and all core chunk subsystems (kind, state, render, edit, resolve).
- Removed chunk-mode CLI/read/edit entrypoints, including `read` command and chunk mode registration/prompt tooling.
- Removed chunk selectors from `read` and `grep` tools, switching behavior to raw/L-range handling.
- Fixed poll wait parsing to keep defaulting to `30s` when the provided value is empty.
- Reorganized edit tool from `patch/` to `edit/` directory with dedicated mode subdirectories (chunk, patch, hashline, replace).
- Replaced line-scoped edit operations with substring-based `find` parameter and added `replace_body` operation for preserving signatures.
- Added chunk focus modes (Expanded, Collapsed, Container) and focused rendering to display only touched chunks and adjacent siblings.
- Implemented notebook (ipynb) language support with virtual source conversion and cell-based chunk parsing.
- Enhanced chunk edit error messages with consistent checksum mismatch reporting and improved chunk selector auto-resolution.
- Extracted edit mode implementations into separate modules with improved helper functions and LSP integration for diagnostics.
- Refactored filesystem scan cache integration to use pre-scanned entries from fs_cache module instead of manual directory walking in grep.rs.
- Extracted filesystem scan cache invalidation helpers into dedicated fs-cache-invalidation.ts module with three functions: invalidateFsScanAfterWrite, invalidateFsScanAfterDelete, and invalidateFsScanAfterRename.
- Centralized file mention discovery profile configuration into getMentionCandidateDiscoveryProfile() function for improved maintainability.
- Added comprehensive documentation of filesystem-scan cache architecture contract including cache key specifications, TTL policies, and invalidation patterns.
- Updated CHANGELOG.md to document filesystem scan cache invalidation helpers and named discovery profile for file mention candidates.
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