Runtime re-seeds BOOTSTRAP.md after onboarding (idempotency regression)

[wenakita]

Summary

In production use, a configured agent can be pushed with workspace/BOOTSTRAP.md removed, but runtime lifecycle events still reintroduce bootstrap behavior and trigger repeated onboarding loops.

Expected behavior

• BOOTSTRAP.md is first-run only.
• After onboarding and deletion, startup should never re-run onboarding for already configured identity.
• Runtime should not mutate workspace prompts back into onboarding state.

Actual behavior

• BOOTSTRAP.md can reappear after restart/probe cycles.
• Agent re-enters identity onboarding flow ("who am I?" style prompts) despite prior configuration.
• During repro attempts, control paths also showed intermittent runtime instability (chat hangs / 500s), which makes drift hard to recover from reliably.

Reproduction (high level)

1. Start from template-derived agent with configured identity.
2. Remove workspace/BOOTSTRAP.md and push.
3. Restart agent and verify bootstrap is absent.
4. Run normal chat/probe activity.
5. Observe bootstrap/onboarding behavior return unexpectedly.

Impact

• Breaks deterministic production agent behavior.
• Causes user-facing regressions and identity churn.
• Increases operational overhead due to repeated manual re-apply/restart loops.

Mitigation PR

A template-level mitigation is proposed here (idempotent bootstrap guard):

• Make BOOTSTRAP idempotent for reseeded workspaces #1

This mitigation reduces user impact by skipping onboarding if identity markers are already configured, but does not replace a runtime/platform fix if file reseeding persists.

Additional external evidence

• Repro + timeline from a live agent incident:
  • https://github.com/wenakita/4626-og-agent-xnz7fxas/pull/1

[obo20]

@wenakita thank you for the report. This should be fixed in a recent upgrade made last friday to our infrastructure. Can you double check you're still having this issue without the BOOTSTRAP.md changes you proposed?