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fix(upgrade): leave agent surfaces alone unless --refresh-agents is passed - #333
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…assed `codegraph-vba upgrade` now skips the agent refresh and the Claude prompt hook by default. `--refresh-agents` restores that behaviour and the existing environment kill-switches still apply under it. `install` and `install --refresh` no longer write the CodeGraph block into an instruction file that already carries a gentle-ai marker. The file is reported as skipped, and other files are unaffected. The upgrade summary lists the agent surfaces it did not touch. Refs #332
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Summary
codegraph upgradeno longer rewrites agent surfaces by default. Instructions blocks, MCP entries and hooks are left as they are unless--refresh-agentsis passed, andinstallskips any file that carries a<!-- gentle-ai:marker. Skills directories are never touched byupgradeorinstall, with or without the refresh flag.Why
Upgrading to 2.1.1 added a
<!-- CODEGRAPH_START -->block to the globalCLAUDE.md/AGENTS.mdfiles that gentle-ai manages, contradicting the CodeGraph guidance gentle-ai already installs there.Changes
upgrade: agent-surface refresh is opt-in via--refresh-agents.install: skips files containing agentle-ai:marker;--refreshkeeps that guard.__tests__/upgrade-agent-surfaces.test.ts(default upgrade,--refresh-agents, install, install--refresh, gentle-ai marker skip, skills directories unchanged) and an adjusted__tests__/upgrade.test.ts.Testing
npx vitest run __tests__/upgrade-agent-surfaces.test.ts __tests__/upgrade.test.ts: 80 tests pass, run with an isolatedHOME.Closes #332