chore: prepare 0.12.1 patch releases

[jlitola]

Summary

• bump githits and @githits/mcp from 0.12.0 to 0.12.1
• consolidate all three pending fragments into artifact-specific 2026-09-04 changelog sections
• regenerate versioned plugin, assistant, and MCP registry manifests from canonical release metadata
• correct the Phase 2 plan status now that PR feat: expose actionable dependency issues #351 is merged
• record the maintainer-approved patch classification for the additive package-intelligence capabilities, overriding the fragments' original minor impact

Validation

• bun test (3,976 pass, 0 fail)
• bun run plugins:check
• bun run typecheck
• bun run lint
• bun run format:check
• bun run build
• bun run validate:packages
• bun run validate:packages:mcp-publish
• bun run smoke:cli (103 live steps)
• bun run smoke:mcp (54 live steps)
• bun run smoke:cli:built (23 unauthenticated Node steps)
• bun run smoke:mcp:built (8 registration steps)
• pinned mcp-publisher v1.7.9 validation of server.json
• npm and Git tag collision checks for both 0.12.1 artifacts
• git diff --check

The package validation publish dry-run passed on its first run. A concurrently launched standard validation initially received non-JSON output from npm pack; its isolated rerun completed successfully. Targeted Codex descriptor evaluations for the behavior changes passed in their feature PRs and are recorded in the active implementation plan; no release-metadata behavior changed here.

Merge gate

Do not merge or enable auto-merge without separate explicit human approval for this release PR.