Add theming, app icon, and Obsidian parity foundations

[cwilson613]

Summary

• Adds tweakcn-backed UI theming with built-in presets and broader theme token mapping.
• Replaces Codex-era app icon assets with the new Flynt stone/iron mark across desktop, macOS ICNS, and iOS app icon sets.
• Adds the Obsidian parity foundation pass: active-note history/recovery, Git snapshot flow, sync activity diagnostics, toolbar/command palette entry points, and parity planning docs.
• Adds OP-04 publication authoring workflow: editable per-note publication fields in Properties, safe [publication] frontmatter writes, local preview export command/report modal, and publication adapter contract docs.
• Adds OP-05 bookmarks and saved searches: portable .flynt/bookmarks.toml, sidebar bookmark list, note/search bookmark commands, saved-search route restore, and store round-trip tests.
• Adds OP-06 Project Lenses: portable .flynt/lenses/*.toml definitions, live document/task lens execution over existing store APIs, a read-only Lenses route, and Save Search as Lens.
• Adds OP-07 note hover previews: reusable preview card, delayed previews for CodeMirror/rendered wikilinks, and reused previews for search results and sidebar notes.
• Updates onboarding/UI documentation for sync activity, note history, snapshots, publication preview, bookmarks, saved searches, Project Lenses, and page previews.

Validation

• cargo check -p flynt-agent -p flynt-app -p flynt-core -p flynt-store
• cargo test -p flynt-store -p flynt-core -p flynt-agent
• OP-04 focused: cargo check -p flynt-app -p flynt-store
• OP-04 focused: cargo test -p flynt-store publication -- --nocapture
• OP-05 focused: cargo check -p flynt-app -p flynt-store
• OP-05 focused: cargo test -p flynt-store bookmarks -- --nocapture
• OP-06 focused: cargo check -p flynt-app -p flynt-store -p flynt-core
• OP-06 focused: cargo test -p flynt-core lens -- --nocapture
• OP-06 focused: cargo test -p flynt-store lenses -- --nocapture
• OP-07 focused: cargo check -p flynt-app
• OP-07 focused: cargo test -p flynt-app note_preview -- --nocapture
• OP-07 focused: git diff --check
• Previous icon/theme validation on this branch: python3 scripts/generate-icons.py, python3 -m py_compile scripts/generate-icons.py, cargo check -p flynt-app, cargo test -p flynt-app theme::

Notes

This draft is rebased onto current main, including the merged MCP/tab latency hotfix from #19.

OP-07 graph hover previews and visual e2e smoke are still marked as follow-up work in the parity milestone.

[github-advanced-security]

lipstyk found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.