[WS1.2] Audit and minimize scattered core file modifications #165

Parent: #158

Context

The full fork audit found 31 conflict-prone files where both our fork AND upstream made changes. Beyond the session/ files already addressed, these core files are modified:

Modified core files needing audit

• src/agent/agent.ts — unknown changes
• src/bun/index.ts — unknown changes
• src/config/config.ts — unknown changes
• src/flag/flag.ts — unknown changes
• src/skill/skill.ts — unknown changes
• src/plugin/codex.ts — unknown changes
• src/plugin/copilot.ts — 1M context related
• src/provider/provider.ts — 1M context headers + limit override
• src/provider/transform.ts — Opus 4.6 effort parameter
• src/cli/cmd/run.ts — unknown changes
• src/cli/cmd/tui/app.tsx — unknown changes
• src/cli/cmd/tui/routes/session/index.tsx — unknown changes (rg TUI rendering?)
• src/cli/cmd/tui/util/clipboard.ts — unknown changes

Tests modified

• config.test.ts, skill.test.ts

Goal

For each file:

1. Classify the change (async-task / rg-tool / 1M-context / fork-improvement / unnecessary)
2. Revert unnecessary changes to match upstream
3. Document why each remaining change exists

Acceptance Criteria

• Every modified core file classified
• Unnecessary changes reverted
• Remaining changes documented in fork-features.json (WS2)
• Diff reduced to minimum necessary