v2 - #141
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Replace full DOM teardown+rebuild with persistent shell and keyed row maps. TreeRenderer becomes PublicationTree class with mount()/update() lifecycle. DiffModal uses persistent header with replaceable content pane. ScrollSync now handles both vertical and horizontal scrolling. Indeterminate checkbox CSS styling added. All files selectable including published. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Remove stubbed RepositoryConnection class entirely. Add QuartzFileSource interface with RemoteFileSource (git remote) and LocalFileSource (local disk) implementations. Extract static methods to GitRemoteUtils with isomorphic-git HTTP transport. Migrate all 15 consuming files (10 source + 5 test). Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
NodeDetector checks Node.js >= 18 availability with session caching. QuartzRepoValidator checks quartzRepoPath for package.json and Quartz config. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Gate Quartz settings page to desktop only. Add setup wizard and manual setup commands with platform guards. Migrate Platform.isDesktop to Platform.isDesktopApp in external-fs. Mark 5 unused settings as deprecated, add schema v3 and v4 migrations. Add persistent notice and settings action for unconfigured repos. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
All 16 console.error calls across 7 integration files changed to console.debug. These are non-fatal errors in catch blocks that already return fallback values. CompilationQueue catch block also captures error variable for logging. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add shared ASSET_EXTENSIONS with isMediaFile/isTextMediaFile/getMediaIcon. Add MediaLinkResolver to track which media is linked by published notes. Extend PublishStatus with MediaEntry and ArbitraryFileEntry types. Categorize media separately from deleted notes with linked/unlinked status. Add cleanOrphanedMedia, deleteByRepoPaths, publishArbitraryFiles to Publisher. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add ManualSetupModal with URL validation, connection test, provider auto-detection, progressive disclosure, and advanced settings section. Fix setup wizard: paginated repo loading with search, v5 branch for new repos, correct GitHub Pages URL, Done button on success step. Add quartz.config.yaml creation from template defaults with baseUrl. Add content/index.md with welcome page for new repos. Extract detectGitProvider to shared utility. Add getFileContent and updateFile to GitHubApiService. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Change detectAll() from Promise.all to sequential loop to prevent terminatePendingProcess() from killing concurrent detections. Add proactive version warnings for Node.js < 18 and npm < 8. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Replace COMMANDS array with COMMAND_REGISTRY metadata system. Switch from registerObsidianProtocolHandler to registerCliHandler. Add help flag interceptor, base quartz-syncer command, verbose flag. Add shared requireQuartzRunner guard. Rewrite mark handler with glob, fuzzy search, and dry-run support. Add force flag to delete/sync, dry-run to publish/delete/sync. Add verbose output for status/test/publish/delete/sync handlers. Restructure plugin handler: list/add/remove work everywhere, install/enable/disable/config/prune require QuartzRunner. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add timeout sentinel (-1 = no timeout) to ProcessRunner. Add timeout to QuartzRunnerOptions, wire through all methods. Refactor serve() to bypass ProcessRunner singleton pendingProcess. Add sync, restore, pluginInstall/Enable/Disable/Config/Prune methods. Add quartz-build, quartz-serve, quartz-sync, quartz-restore handlers. Add circuit breaker auto-recovery after 5 minute cooldown. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add pauseAutoPublish/resumeAutoPublish to BackgroundEngine. Publication Center pauses auto-publish on open, resumes on close. Prevents race condition where auto-publish modifies files user is selecting. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Remove stale RepositoryConnection references and outdated CLI count. Document two-tier platform split, publication model, CLI registration via registerCliHandler, Quartz v5 config conventions, and working with external systems directive. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Publisher refactoring: - Extract PublishBackend interface with RemotePublishBackend and LocalPublishBackend - Extend QuartzFileSource with writeBinaryFile, deleteFile, listAllFiles - Refactor Publisher from GitBackend to PublishBackend abstraction - Wire local mode into getPublisher (quartzRepoPath takes priority) - Expose cliHandlers on plugin instance for test invocation New CLI commands: - quartz-syncer:repo (info, set-local, set-remote, verify) - quartz-syncer:media (list, orphaned, clean) - quartz-syncer:diff (compiled vault vs repo content) - quartz-syncer:validate (repo health checks with lockfile warning) - quartz-syncer:inspect (cache, hashes, compilation, queue) CLI gap filling: - Cache handler: export, import, prune actions - Config handler: reset action (partial, preserves identity fields) - Plugin handler: add/remove dry-run via structuredClone, search action - Publish/sync/delete: custom commit message param - Publish: action=arbitrary for non-content file publishing - Test handler: local mode path verification - Inspect handler: target=queue via getEngineStatus - Status handler: verbose enrichment with publishFlag and hasMedia Marketplace migration: - QuartzPluginRegistry: new URL, full marketplace schema - PluginBrowserModal: tags to category filter migration E2E test harness: - 6 Quartz repo fixtures (minimal through multi-plugin) - 3 vault templates (basic, media-heavy, bulk) - FixtureManager, RepoAssertions, CLI invoker helpers - 44 scenario specs across 10 spec files (43 passing) - wdio.conf.mts extended for scenario specs Unit tests: 522 total (41 new for CLI gap coverage)
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