_{Reviews (2): Last reviewed commit: "Disable replicated workflow run actions" | Re-trigger Greptile}

_{Reviews (3): Last reviewed commit: "Trust SSH host keys on first use" | Re-trigger Greptile}

_{Reviews (4): Last reviewed commit: "Honor replicated workflow run timeouts" | Re-trigger Greptile}

_{Reviews (5): Last reviewed commit: "Stabilize Linear E2E workflow triggers" | Re-trigger Greptile}

Greptile Summary

This PR adds on_enter.run support for workflow pipeline stages, allowing a shell command to execute in the agent workspace before the stage's inject and other on-enter actions proceed. It also replaces all InsecureIgnoreHostKey SSH usages with a trust-on-first-use store backed by a new ssh_known_hosts SQLite table, resolving the previously flagged host-verification gap using an INSERT OR IGNORE + SELECT pattern to handle concurrent first-use safely.

• Pipeline run action: executePipelineRunAction dispatches to Daytona, exe.dev, Replicated (SSH), or a noop provider; runOnEnter runs the command synchronously before inject, and respects continue_on_error to either surface an error and abort or warn and continue.
• SSH TOFU: verifySSHHostKeyOnce uses INSERT OR IGNORE to atomically handle concurrent first-use writes, then SELECT-compares the persisted key; a retry loop with back-off handles SQLite busy errors.
• E2E test isolation: Linear E2E tests now create and clean up a per-run label, scoping issue triggers to avoid cross-run interference.

Confidence Score: 5/5

Safe to merge; all three previously flagged SSH and timeout issues are addressed, and no new blocking defects were found.

The InsecureIgnoreHostKey removals are complete across all four SSH call sites, the TOCTOU race is closed with INSERT OR IGNORE, and the replicated-provider timeout is now enforced via sshRunWithTimeout. The remaining findings are minor nits that do not affect correctness on the critical paths.

ssh_known_hosts.go (isSQLiteBusy coverage) and pipeline_runner.go (exedev timeout precision) are worth a quick second look, but neither blocks the change.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[Stage transition triggered] --> B[claimPipelineStageTransition]
    B -- duplicate --> C[return false]
    B -- claimed --> D{OnEnter.Run.Command set?}
    D -- no --> H
    D -- yes --> E[executePipelineRunAction]
    E --> F{provider}
    F -- daytona --> G1[ExecWithTimeout ctx+30s outer / timeout inner]
    F -- exedev --> G2[Exec ctx+30s outer only]
    F -- replicated --> G3[sshRunWithTimeout with timer = timeout]
    F -- noop --> G4[return success]
    G1 & G2 & G3 & G4 --> I{exit code 0 and no error?}
    I -- yes --> H[runOnEnter: send Inject, MoveIssue, etc.]
    I -- no, continue_on_error=true --> J[injectHubMessage: Warning] --> H
    I -- no, continue_on_error=false --> K[injectHubMessage: Error, return early]
    H --> L[transitionPipelineStageWithContext returns true]
    K --> L
    L --> M{Terminal stage?}
    M -- no --> N[Done]
    M -- yes --> O[Wait for streaming, checkpoint, delete claw]

_{Reviews (6): Last reviewed commit: "Avoid known host first-use race" | Re-trigger Greptile}