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chore(deps): patch + minor bumps across the monorepo (Task #135) (#1656)

* chore(deps): apply patch + minor bumps across monorepo

Refresh dependencies up to the latest version within the current major
across the root and every workspace package. Lockfile regenerated.

Bumps applied (manifests):
- root: @biomejs/biome 2.4.12 → 2.4.13, knip 6.4.1 → 6.7.0,
  oxlint 1.60.0 → 1.61.0
- cli: hono 4.12.14 → 4.12.15, vite 8.0.8 → 8.0.10,
  @types/bun 1.3.12 → 1.3.13
- daemon: @openai/codex 0.121.0 → 0.125.0, @types/bun 1.3.12 → 1.3.13
- shared: @types/bun 1.3.12 → 1.3.13
- ui: @tailwindcss/vite, tailwindcss 4.2.2 → 4.2.4;
  @vitest/coverage-v8, vitest 4.1.4 → 4.1.5;
  vite 8.0.8 → 8.0.10; lucide-preact 1.8.0 → 1.11.0;
  @types/bun 1.3.12 → 1.3.13
- web: marked 18.0.0 → 18.0.2;
  @tailwindcss/vite, tailwindcss 4.2.2 → 4.2.4;
  @vitest/coverage-v8, @vitest/ui, vitest 4.1.4 → 4.1.5;
  vite 8.0.8 → 8.0.10; @types/bun 1.3.12 → 1.3.13

Reverted (surfaced for human review in the PR description):
- @anthropic-ai/claude-agent-sdk 0.2.112 (declined 0.2.119 — vendored
  SDK type file in packages/shared/src/sdk/sdk.d.ts diverges by ~600
  lines)
- @github/copilot-sdk 0.2.2 (declined 0.3.0 — 0.x minor with
  PermissionDecision API redesign)

No format/lint reflow required. `bun run check` and the daemon, web,
and shared package tests are green.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* ci: unify bun version to 1.3.13 across workflows

main.yml was on 1.3.11 (8 occurrences) and release.yml on 1.3.10 (2
occurrences). Standardize on 1.3.13 (current latest, matches local
development) so all CI jobs run on the same Bun runtime.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

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Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

9279 of 12457 branches covered (74.49%)

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