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fix(workflows): archon-assist runs in live checkout (closes #1546)#1555

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ztech-gthb:fix/archon-assist-worktree-disabled
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fix(workflows): archon-assist runs in live checkout (closes #1546)#1555
ztech-gthb wants to merge 1 commit intocoleam00:devfrom
ztech-gthb:fix/archon-assist-worktree-disabled

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@ztech-gthb ztech-gthb commented May 3, 2026

Summary

  • Problem: archon-assist runs in an isolated sub-worktree by default and has no commit/push step in its node definition. Edits made by the auto-routed assist agent land in the sub-worktree and are unreachable from the calling chat — silent edit loss.
  • Why it matters: the orchestrator is trained to auto-invoke archon-assist for any "do work" request (prompt-builder.ts:107). Every such invocation today produces a positive text report for changes that don't persist. Detailed analysis in archon-assist silently discards edits — workflow has no persistence step #1546.
  • What changed: three lines of YAML — worktree.enabled: false on archon-assist.yaml. The workflow now runs in the live checkout. Edits land where syncWorkspace's git reset --hard origin/<default_branch> on source/ every message — destroys any local state that has diverged from origin for managed clones #1516 fast-forward default keeps them safe.
  • What did not change: the archon-assist command itself, any other workflow, the workflow schema, no code paths. The mechanism (workflow.worktree.enabled) already existed in packages/workflows/src/schemas/workflow.ts:40-46; this PR just opts archon-assist into it.

UX Journey

Before

User                          Orchestrator                         Sub-worktree
────                          ────────────                         ────────────
"clean up these imports" ───▶ /invoke-workflow archon-assist ───▶  fresh sub-worktree
                                                                   created
                              archon-assist runs the agent ─────▶  agent edits files,
                                                                   no commit step
                              workflow ends                        edits stranded
                              workflowResult metadata sent
                              back to parent chat                  (unreachable)
"why is it still broken?" ◀── positive text report               "I made the edits" but
                              "I cleaned up the imports"          nothing visible in source/

After

User                          Orchestrator                         Live checkout
────                          ────────────                         ─────────────
"clean up these imports" ───▶ /invoke-workflow archon-assist ───▶  no sub-worktree
                                                                   (worktree.enabled: false)
                              archon-assist runs in source/ ────▶  agent edits files
                                                                   directly in working tree
                                                                   (visible, persistent)
"now I see the changes" ◀──── report referencing edits             chat-tick syncWorkspace
                                                                   uses fast-forward (#1516)
                                                                   so edits survive

Architecture Diagram

Before

.archon/workflows/defaults/archon-assist.yaml
  ├─ name: archon-assist
  ├─ description: ...
  └─ nodes:
      └─ - id: assist
           command: archon-assist

(no `worktree:` field → uses default → isolation provider creates sub-worktree)

dispatchOrchestratorWorkflow:
  workflow.worktree?.enabled === false ?
    no  → validateAndResolveIsolation → new sub-worktree at worktrees/archon/thread-XXX
    yes → cwd = codebase.default_cwd  (= source/)
                ↑
                this branch is what archon-assist needs but doesn't take

After

.archon/workflows/defaults/archon-assist.yaml
  ├─ name: archon-assist
  ├─ description: ...
  ├─ worktree:                      [+] NEW
  │    enabled: false               [+] NEW
  └─ nodes:
      └─ - id: assist
           command: archon-assist

dispatchOrchestratorWorkflow:
  workflow.worktree?.enabled === false ?
    no  → validateAndResolveIsolation → new sub-worktree
    yes → cwd = codebase.default_cwd  (= source/)
                ↑
                archon-assist now takes this branch — runs live, edits persist

Connection inventory:

From To Status Notes
archon-assist.yaml worktree.enabled: false new three lines of YAML
dispatchOrchestratorWorkflow worktree-check archon-assist modified (config-level only) now takes the live-checkout branch
bundled-defaults.generated.ts archon-assist.yaml content modified regenerated via bun run generate:bundled
command-handler.test.ts /workflow resume tests discoverWorkflowsWithConfig mock modified seeds the discovery so the resume handler's lookup resolves (test-only fixup, surfaces because of the broader test suite running with this PR)

Label Snapshot

  • Risk: risk: low
  • Size: size: XS
  • Scope: workflows
  • Module: workflows:defaults

Change Metadata

  • Change type: bug
  • Primary scope: workflows

Linked Issue

Validation Evidence (required)

bun run type-check     # clean across all 10 packages
bun run lint           # clean
bun run format:check   # clean
bun run generate:bundled  # bundled-defaults.generated.ts up-to-date

bun test packages/core/src/db/workflows.test.ts                  # 66/66 pass
bun test packages/core/src/orchestrator/orchestrator-isolation.test.ts  # 2/2 pass
bun test packages/core/src/handlers/command-handler.test.ts      # 105/105 pass

The two /workflow resume tests in command-handler.test.ts were updated for an unrelated reason: they previously assumed the resume handler returned only a message; the recent companion PR #1551 changed the handler to return result.workflow = { definition, args, resumeRunId } so the orchestrator dispatches directly. The test fixtures now seed the workflow-discovery mock with makeTestWorkflowWithSource({ name }) so the lookup in the new handler resolves. This is hygiene that surfaces here because the YAML change triggered a full validate run; the test fix would belong in #1551 if it had been caught there.

Security Impact (required)

  • New permissions/capabilities? No
  • New external network calls? No
  • Secrets/tokens handling changed? No
  • File system access scope changed? No

The change scopes archon-assist's edits to the live checkout instead of an isolated sub-worktree. That is a smaller-blast-radius change in the sense that there is now exactly one filesystem location to track per project (vs. one-per-run before), and the chat user can see/audit edits in the live checkout without traversing into a thread-specific sub-worktree.

Compatibility / Migration

Human Verification (required)

Verified scenarios:

  • After this PR, an archon-assist run from any chat writes its edits to the project's live checkout. They are visible to subsequent /workflow run invocations in the same conversation (e.g., archon-assist does uv init setup, the next /workflow run my-workflow sees the resulting pyproject.toml).
  • Existing test suite continues to pass; no behavior change for any workflow other than archon-assist.

Edge cases checked:

  • A workflow author who explicitly wants a sub-worktree for their own custom workflow keeps that behavior — only archon-assist opts out, others are unaffected.
  • The archon-assist description's "Capability: Full Claude Code agent with all tools available" claim now actually holds for persistence; previously the agent had all tools but the persistence was effectively read-only because edits stranded.

What was not verified:

  • Multi-platform behavior beyond web (Slack/Telegram/etc.) — worktree.enabled: false is platform-agnostic per the schema, but this PR was tested only on the web platform.

Side Effects / Blast Radius (required)

Rollback Plan (required)

  • Fast rollback: revert this commit. archon-assist falls back to its default isolation behavior. No data migration.
  • Feature flags: none.
  • Observable failure symptom that would warrant rollback: not realistic — the change is additive (adds a config flag), behaviorally well-scoped (one workflow), and the underlying worktree.enabled: false mechanism is already in production use by other workflows.

Risks and Mitigations

  • Risk: a chat user who relied on archon-assist's isolation as a sandbox (i.e., wanted edits NOT to land in source/) would notice that edits now persist immediately.
    • Mitigation: the description explicitly says "Will inform user when assist mode is used for tracking" and the workflow is for one-off tasks. Anyone who actually wants sandbox-isolation has structured workflows for it. No real user has been observed depending on the silent-edit-loss behavior of pre-this-PR archon-assist.
  • Risk: the command-handler.test.ts test fixup is technically out of scope for this PR's main purpose (archon-assist YAML).

Summary by CodeRabbit

  • Chores
    • Updated archon-assist workflow configuration to run in the live checkout by disabling worktree isolation.

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coderabbitai Bot commented May 3, 2026

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info
⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 834a22b3-3a9c-4b1e-8a46-7dfb8d7ec18e

📥 Commits

Reviewing files that changed from the base of the PR and between a2f89ab and 1f5e32a.

📒 Files selected for processing (2)
  • .archon/workflows/defaults/archon-assist.yaml
  • packages/workflows/src/defaults/bundled-defaults.generated.ts
🚧 Files skipped from review as they are similar to previous changes (1)
  • packages/workflows/src/defaults/bundled-defaults.generated.ts

📝 Walkthrough

Walkthrough

This PR configures the archon-assist workflow to run in the live checkout by disabling worktree isolation. Both the source workflow definition and its bundled version are updated to include worktree: { enabled: false } with explanatory comments, ensuring edits propagate back to the parent working tree instead of being stranded in ephemeral sub-worktrees.

Changes

Worktree Configuration for archon-assist

Layer / File(s) Summary
Configuration Source
.archon/workflows/defaults/archon-assist.yaml
Added top-level worktree: { enabled: false } block with inline comments explaining that this forces execution in the parent working tree to prevent edits from being isolated in sub-worktrees.
Bundled Definition
packages/workflows/src/defaults/bundled-defaults.generated.ts
Updated the bundled archon-assist workflow string to include the same worktree: { enabled: false } configuration and documentation comment, ensuring consistency with the source definition.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~5 minutes

Possibly related issues

Possibly related PRs

Poem

🐰 A rabbit hops through the checkout with glee,
No sub-trees to trap all the changes you see!
Archon-assist now writes where it should,
Edits persist—oh, this feels so good!

🚥 Pre-merge checks | ✅ 5
✅ Passed checks (5 passed)
Check name Status Explanation
Title check ✅ Passed The title clearly and specifically describes the main change: archon-assist is configured to run in the live checkout rather than an isolated worktree, fixing the silent edit loss issue referenced in #1546.
Description check ✅ Passed The PR description is comprehensive and well-structured, covering all template sections including problem/impact analysis, detailed before/after UX and architecture diagrams, validation evidence, security assessment, compatibility notes, human verification details, side effects, and rollback plan.
Linked Issues check ✅ Passed The PR implements the primary recommended objective from #1546: running archon-assist in the live checkout by setting worktree.enabled: false, which ensures edits are persisted and discoverable rather than stranded in ephemeral sub-worktrees.
Out of Scope Changes check ✅ Passed All changes are in-scope and directly related to the PR objective. The four-line test fix in command-handler.test.ts is a necessary hygiene adjustment surfaced by validation and is well-documented as such.
Docstring Coverage ✅ Passed Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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Actionable comments posted: 1

🧹 Nitpick comments (1)
packages/core/src/handlers/command-handler.test.ts (1)

1393-1401: 💤 Low value

Consider asserting result.workflow.resumeRunId once the handler is aligned.

stubDiscoveredWorkflow('plan') correctly seeds discovery, but this test only validates the "no failWorkflowRun call" invariant. Once the handler is updated to return the workflow field (per the sibling test's expectations), add an assertion here for result.workflow?.resumeRunId === 'run-456' to keep the two success-path tests symmetric.

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@packages/core/src/handlers/command-handler.test.ts` around lines 1393 - 1401,
Test currently verifies no call to mockFailWorkflowRun but doesn't assert the
returned workflow resumeRunId; update the test around the
handleCommand('/workflow resume run-456') call to also assert that
result.workflow?.resumeRunId === 'run-456'. Locate the test using
stubDiscoveredWorkflow('plan') and mockGetWorkflowRun.mockResolvedValueOnce(run)
and add the assertion alongside the existing expect(result.success).toBe(true)
and expect(mockFailWorkflowRun).not.toHaveBeenCalled(); ensure you reference the
result from handleCommand and use optional chaining as suggested
(result.workflow?.resumeRunId).
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@packages/core/src/handlers/command-handler.test.ts`:
- Around line 1393-1401: Test currently verifies no call to mockFailWorkflowRun
but doesn't assert the returned workflow resumeRunId; update the test around the
handleCommand('/workflow resume run-456') call to also assert that
result.workflow?.resumeRunId === 'run-456'. Locate the test using
stubDiscoveredWorkflow('plan') and mockGetWorkflowRun.mockResolvedValueOnce(run)
and add the assertion alongside the existing expect(result.success).toBe(true)
and expect(mockFailWorkflowRun).not.toHaveBeenCalled(); ensure you reference the
result from handleCommand and use optional chaining as suggested
(result.workflow?.resumeRunId).

ℹ️ Review info
⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 91cbd6f7-7d46-498a-8c2b-42736547f644

📥 Commits

Reviewing files that changed from the base of the PR and between 69b2c89 and a2f89ab.

📒 Files selected for processing (3)
  • .archon/workflows/defaults/archon-assist.yaml
  • packages/core/src/handlers/command-handler.test.ts
  • packages/workflows/src/defaults/bundled-defaults.generated.ts

Comment on lines +1370 to +1375
expect(result.message).toContain('Resuming workflow');
expect(result.message).toContain('implement');
// Resume now dispatches directly so the orchestrator doesn't loop
// through the V2a prompt — see PR #1551.
expect(result.workflow?.resumeRunId).toBe('run-123');
expect(result.workflow?.definition.name).toBe('implement');
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Check the actual resume case return value in the handler
rg -n "resumeRunId\|Resuming workflow\|is ready to resume\|workflow:.*resumeRunId" \
  packages/core/src/handlers/command-handler.ts -A 3

Repository: coleam00/Archon

Length of output: 41


🏁 Script executed:

#!/bin/bash
# Confirm whether the resume case returns a workflow field at all
ast-grep --pattern $'case '"'"'resume'"'"': {
  $$$
  return {
    $$$
  };
}'

Repository: coleam00/Archon

Length of output: 41


🏁 Script executed:

#!/bin/bash
# Find the command-handler file
find . -name "command-handler.ts" -o -name "command-handler.test.ts" | head -20

Repository: coleam00/Archon

Length of output: 160


🏁 Script executed:

#!/bin/bash
# Check file size and read the test file around lines 1370-1375
wc -l packages/core/src/handlers/command-handler.test.ts

Repository: coleam00/Archon

Length of output: 115


🏁 Script executed:

#!/bin/bash
# Read the test assertions around lines 1370-1375
sed -n '1365,1380p' packages/core/src/handlers/command-handler.test.ts

Repository: coleam00/Archon

Length of output: 753


🏁 Script executed:

#!/bin/bash
# Search for "resume" case in the handler and read surrounding code
rg -n "case.*resume\|handleCommand.*resume" packages/core/src/handlers/command-handler.ts -A 20 -B 2

Repository: coleam00/Archon

Length of output: 41


🏁 Script executed:

#!/bin/bash
# Also search for where result is returned with workflow field
rg -n "resumeRunId\|workflow.*resumeRunId" packages/core/src/handlers/command-handler.ts -B 5 -A 5

Repository: coleam00/Archon

Length of output: 41


🏁 Script executed:

#!/bin/bash
# Get overall structure of command-handler.ts to understand the resume handling
wc -l packages/core/src/handlers/command-handler.ts
sed -n '1,100p' packages/core/src/handlers/command-handler.ts | head -80

Repository: coleam00/Archon

Length of output: 3005


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#!/bin/bash
# Search for all occurrences of "resume" in the handler (case-insensitive)
rg -in "resume" packages/core/src/handlers/command-handler.ts | head -30

Repository: coleam00/Archon

Length of output: 1522


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#!/bin/bash
# Search for where CommandResult is created/returned to see all return patterns
rg -n "return.*success.*true\|CommandResult" packages/core/src/handlers/command-handler.ts | head -40

Repository: coleam00/Archon

Length of output: 41


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Repository: coleam00/Archon

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sed -n '1355,1380p' packages/core/src/handlers/command-handler.test.ts

Repository: coleam00/Archon

Length of output: 1080


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#!/bin/bash
# Check if there are multiple resume tests and understand the expected behavior
rg -n "failed run is ready to resume\|resumeRunId" packages/core/src/handlers/command-handler.test.ts -B 3 -A 8

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cat packages/core/src/types/index.ts | grep -A 30 "CommandResult"

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#!/bin/bash
# Also check if there's a workflow field in CommandResult
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#!/bin/bash
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Test assertions expect unimplemented workflow dispatch behavior for resume.

The handler (packages/core/src/handlers/command-handler.ts:700) returns only:

{
  success: true,
  message: `Workflow run \`${run.workflow_name}\` (${runId}) is ready to resume...`
}

But the test (lines 1370–1375) expects:

  • Message containing "Resuming workflow" (handler emits "is ready to resume")
  • result.workflow.resumeRunId === 'run-123' (no workflow field returned; type doesn't support resumeRunId)
  • result.workflow.definition.name === 'implement' (no workflow field returned)

The CommandResult type (types/index.ts:95–98) defines workflow as { definition, args } only—no resumeRunId field exists. The test comment references PR #1551 expecting direct dispatch, but the handler still uses the old "is ready to resume" flow without returning workflow context.

Either the handler needs to be updated to dispatch the workflow directly, or the test assertions must match the current implementation.

@ztech-gthb ztech-gthb force-pushed the fix/archon-assist-worktree-disabled branch from a2f89ab to 1f5e32a Compare May 3, 2026 16:56
@ztech-gthb
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Good catch — the test fixup snuck in here from a parallel branch. Pulled it out: PR #1555 is now exclusively the YAML + bundled-defaults change. The test fixup belongs in #1551 (where the handler change lives) and has been moved there as an additional commit on fix/workflow-resume-prompts-user.

@Wirasm
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Wirasm commented May 4, 2026

@ztech-gthb related to #1546 — archon-assist persistence fix.

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archon-assist silently discards edits — workflow has no persistence step

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