- migrate_to_workspace: preserve legacy flat notes even without canonical index
- migrate_to_workspace: reconcile legacy library-record do_ocr/analyze flags including false overrides
- migrate_to_workspace: handle non-canonical legacy filenames via frontmatter title
- asset_index: only advertise fulltext_path/deep_reading_path when files exist
- asset_index: prefer note frontmatter over legacy library-records, fall back to legacy
- setup_wizard: require Python >=3.10 instead of >=3.8
- plugin main.js: align Python version messaging to 3.10+
- ocr.py: auto_analyze_after_ocr reads from formal note paths, not library-records
- HARDEN-04: Pass PADDLEOCR_API_TOKEN via env var instead of CLI --paddleocr-key
- HARDEN-05: Replace innerHTML with createEl() DOM API for directory tree rendering
- Move Better BibTeX auto-export to post-install step (exports dir created by setup)
- Clarify wizard overview: show resources_dir/literature_dir/control_dir hierarchy
- Fix post-install flow order: BBT export → enable plugin → dashboard → sync
- Split do_ocr and analyze marks into separate steps (OCR before deep-reading)
- Mark all literature flags via Base views, not manual file editing
- Make installer incremental: preserve existing files, only create missing ones
- Remove destructive junction/link deletion in TUI wizard
- Merge .env instead of overwriting; skip overwrite for AGENTS.md, docs, plugin
- Update TUI, headless, and plugin completion output to match corrected flow
- Add regression test for non-destructive setup behavior
- Metric cards row: papers count, fulltext-ready (with progress bar), deep-read (with progress bar)
- Lifecycle distribution bar chart via _renderBarChart()
- Aggregated health overview via _renderCollectionHealth() showing PDF/OCR/Note/Asset counts
- Single-pass aggregation from domain-filtered canonical index entries
- Empty state via _renderEmptyState() when domain has no items
- Add _setupEventSubscriptions() for active-leaf-change (debounced 300ms) and vault modify (filtered to formal-library.json)
- Add _renderModeHeader() with mode badge (global/paper/collection classes) and context name
- Add mode warning for paper not found in index (D-18)
- Refactor onOpen() to call _setupEventSubscriptions() before _detectAndSwitch()
- Refactor onClose() with full cleanup: workspace/vault off(), clearTimeout, null cached data
- Refactor constructor with _currentMode, _currentDomain, _currentPaperKey, _currentPaperEntry state
- Refactor onOpen() to call _detectAndSwitch() for initial data load
- Refactor _buildPanel() with _modeContextEl, _contentEl, _actionsGrid elements
- Add _renderActions() extracted from old _buildPanel action loop
- Add _invalidateIndex() to clear cached index
- Add _detectAndSwitch() for active file type detection (D-01..D-04)
- Add _switchMode() for mode-based content rendering (D-05..D-06)
- Add _renderGlobalMode() with OCR section instance vars for _renderOcr compat
- Add _renderPaperMode() placeholder for Phase 29
- Add _renderCollectionMode() placeholder for Phase 30
- Add _refreshCurrentMode() for index change re-render
- Remove orphaned duplicate code block and duplicate _showMessage
- Clean up double closing brace from orphan removal
- _loadIndex(): reads formal-library.json, returns parsed JSON or null
- _getCachedIndex(): lazy-loads and caches items array in this._cachedItems
- _findEntry(key): look up single paper by zotero_key, returns entry or null
- _filterByDomain(domain): filters index items by domain field
Task 1: Add _renderSkeleton, _renderEmptyState, _buildMetricBar utilities + enhanced _renderStats with null guard and progress bar
Task 2: Add _renderLifecycleStepper (6-stage) and _renderHealthMatrix (2x2 grid) methods
Task 3: Add _renderMaturityGauge (6-segment) and _renderBarChart (horizontal bars) methods
All methods use createEl() DOM API, gracefully handle null/undefined via loading skeleton or empty state, and produce CSS classes matching Plan 27-01.
- Section 7: Loading skeleton with @keyframes paperforge-shimmer (1.5s)
- Section 7: Empty state with muted italic styling via .paperforge-empty-state
- Section 2 enhanced: opacity 0.3s transition on metric-card and metric-value
- Added .paperforge-metric-progress and .paperforge-metric-progress-fill for optional progress bar
- All colors use var(--*) Obsidian CSS variables
- Replace Python CLI spawn with fs.readFileSync for primary path
- Single-pass aggregation of lifecycle, health, and OCR counts per D-06
- Fallback to CLI spawn when index file is missing (D-07)
- Add fs and path as top-level requires
- Access system_dir via app.plugins.plugins['paperforge'].settings
- Added _pfConfig cache and _refreshPfConfig() to PaperForgeSettingTab constructor
- display() now calls _refreshPfConfig() at start for fresh path config
- Config Summary section reads path values from _pfConfig (paperforge.json source)
- Prep export path hint now reads from _pfConfig.system_dir
- Non-path fields (paddleocr_api_key, zotero_data_dir) still read from plugin.settings
