fix: resolve import, file refresh, patch diff, and ui/docs regressions

[6crucified]

Issue for this PR

Closes #15797
Closes #15996
Closes #15897
Closes #14964
Closes #14965
Closes #15961

Type of change

• Bug fix
• New feature
• Refactor / code improvement
• Documentation

What does this PR do?

this fixes a batch of reported issues across cli/app/ui/docs:

• opencode import now writes the current instance project_id and directory during import (and conflict update), so imported sessions are attached to the right project/worktree.
• file tabs now refresh when a file.edited event comes in, so edits made by ai appear without reopening the tab.
• apply_patch now reports final diff/files from post-write disk state, so formatter-side edits are included in the returned diff metadata.
• tui theme startup only resolves system palette when theme is actually system (also removed debug noise).
• permission action buttons in message footer now wrap instead of overflowing on narrow layouts.
• skills docs were updated to match current implementation behavior (skills.paths, skills.urls, cache/output details).

why this works:

• each fix is done at the source of the mismatch (import assignment, watcher event handling, post-write diff calculation, theme condition checks, css wrapping, docs content), with tests added/updated for the behavior changes.

How did you verify your code works?

• ran ./script/verify-issues.sh (pass)
• ran targeted tests:
  • packages/opencode: bun test test/cli/import.test.ts test/tool/apply_patch.test.ts
  • packages/app: bun test src/context/file/watcher.test.ts
• ran pre-push bun turbo typecheck (pass)
• manually validated [BUG] opencode import always assigns session to global project, ignoring current working directory #15797 import flow via sqlite row check (project_id, directory)

Screenshots / recordings

not included yet. i can add a short recording for the ui behavior (#15996 / #14965) if maintainers want it.

Checklist

• I have tested my changes locally
• I have not included unrelated changes in this PR

[github-actions]

Hey! Your PR title Fix import/session metadata, live file refresh, apply_patch final diff, and ui/docs regressions doesn't follow conventional commit format.

Please update it to start with one of:

• feat: or feat(scope): new feature
• fix: or fix(scope): bug fix
• docs: or docs(scope): documentation changes
• chore: or chore(scope): maintenance tasks
• refactor: or refactor(scope): code refactoring
• test: or test(scope): adding or updating tests

Where scope is the package name (e.g., app, desktop, opencode).

See CONTRIBUTING.md for details.

[github-actions]

Thanks for updating your PR! It now meets our contributing guidelines. 👍