[namastex888]

The bug I hit

I have a real agent on disk at workspace/agents/omni/AGENTS.md. Every other agent in that directory shows up in genie ls. Omni doesn't. genie spawn omni says:

Error: Agent "omni" not found in directory or built-ins.
  Register with: genie dir add omni --dir <path>

Running genie dir sync manually instantly registered 15 agents that had been invisible — omni plus totvs, helena, researchers, 5 sub-agents, etc. So the sync code works. Something was preventing it from running on serve startup.

Root cause

startAgentSync() in serve.ts silently returned null when findWorkspace() returned null. That disabled the entire auto-discovery subsystem — both the startup sync and the file watcher — for the whole serve lifetime. No warning, no log, no entry in genie serve status.

Why was findWorkspace() returning null? Because ~/.genie/config.json had this persisted from an old test run:

"workspaceRoot": "/tmp/genie-workspace-test-1775349146465-185rx3i66o8"

saveWorkspaceRoot() had written it, /tmp got cleaned, and the fallback path in findWorkspace() has been returning a dead path ever since. Any genie serve booted from outside the real workspace walked up, failed, fell back to the stale path, existsSync returned false, returned null, startAgentSync silently exited. For however long that serve instance ran.

The fix

Three small, contained changes — all behind existing function boundaries:

src/lib/workspace.ts

• saveWorkspaceRoot() refuses to persist paths under os.tmpdir(). Test workspaces can no longer poison the global fallback. Future test runs write their tmp path and the guard drops it on the floor.
• loadWorkspaceRoot() self-heals — if the saved path no longer has a .genie/workspace.json marker, scrub it from config instead of returning a dead fallback forever.
• GENIE_HOME is now resolved lazily via genieHome() instead of a module-level const. Tests can override it per-test via process.env.GENIE_HOME. Without this change, the previous module-level capture meant test env overrides were silently ignored — I caught it because my first test run ended up scrubbing my real ~/.genie/config.json (which, happy accident, was exactly the stale tmp path that originally caused this bug).

src/term-commands/serve.ts

• startAgentSync() logs loudly when workspace is unresolved, with actionable fix guidance, instead of silently returning null:

  Agent sync: DISABLED — no workspace found from cwd or ~/.genie/config.json
    Fix: `cd <workspace> && genie serve restart`, or run `genie init` to bootstrap one
  

• Surfaces per-agent errors from syncResult.errors[] so a single agent with bad frontmatter doesn't vanish silently. Today those errors are collected by syncAgentDirectory() and never printed on the serve-startup path.
• Includes the resolved workspace root in the success log so "which workspace did serve attach to" is visible at a glance, and flags watcher install failures with a warning instead of swallowing them.

src/lib/workspace.test.ts

• Two new tests covering the tmp-path guard and stale-path self-heal.
• All tests now isolate GENIE_HOME per-test so they don't touch (or get contaminated by) the developer's real ~/.genie/config.json.

Scope I deliberately did NOT include

While diagnosing this with the user, we identified 6 DX improvements. This PR implements only the 3 that directly address the silent-failure root cause. The other 3 — which are good ideas but larger surface-area changes — are left for follow-ups:

1. genie spawn <name> should fall back to scanning disk when PG returns null (friendlier error with "found but not registered" message).
2. genie serve status should expose agent-sync/watcher health as a first-class line.
3. genie ls should have an "UNREGISTERED (on disk, not in directory)" section for agents that exist but failed validation.

These are each worth a separate focused PR.

Verification

• bun test src/lib/workspace.test.ts → 12 pass, 0 fail (10 existing + 2 new)
• bun test src/lib/ → 1571 pass, 0 fail
• bunx tsc --noEmit → clean
• bunx biome check src/lib/workspace.ts src/lib/workspace.test.ts src/term-commands/serve.ts → 0 errors, 1 pre-existing warning on startForeground complexity (unrelated, confirmed present on base dev before my changes via git stash round-trip)
• Pre-push hook ran the full 2073-test suite: 0 fail
• Manually verified the omni case end-to-end: genie dir sync from the real workspace root registered 15 previously-invisible agents including omni; genie spawn omni now resolves

Test plan

• bun test src/lib/workspace.test.ts passes
• Full bun test passes (2073/2073)
• bunx tsc --noEmit clean
• bunx biome check 0 errors on changed files
• Manual: start genie serve from outside a workspace → see Agent sync: DISABLED warning with fix guidance
• Manual: start genie serve from inside a workspace → see Agent sync: up to date (workspace: …) line
• Manual: add an invalid frontmatter AGENTS.md, run genie dir sync or restart serve → see the per-agent error line instead of the file silently going missing

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[gemini-code-assist]

Code Review

This pull request enhances workspace configuration handling by introducing a self-healing mechanism for stale workspace roots and preventing the persistence of temporary paths to the global configuration. Additionally, it improves the observability of the genie serve command through more detailed logging and warnings during agent synchronization. Review feedback recommends using realpathSync to correctly identify temporary directories on systems with symlinked temp paths and suggests dynamically resolving the configuration file path in user-facing warnings for better accuracy when GENIE_HOME is customized.

[gemini-code-assist]

On macOS and some other Unix systems, the system temporary directory (e.g., /tmp or /var/folders/...) is often a symbolic link. Since resolve() does not resolve symlinks, isTempPath might return false even for paths within the temporary directory if they are accessed via their real (canonical) path. This would bypass the protection against 'poisoning' the global config. Using realpathSync ensures a robust comparison. Note: Since the top-level imports cannot be modified in this diff, require is used here for a self-contained suggestion.

function isTempPath(root: string): boolean {
  try {
    const { realpathSync } = require('node:fs');
    const normalizedTmp = realpathSync(tmpdir());
    const normalizedRoot = realpathSync(root);
    return normalizedRoot === normalizedTmp || normalizedRoot.startsWith(normalizedTmp + sep);
  } catch {
    return false;
  }
}

References

1. Use dynamic imports (require() or import()) to break circular dependency cycles that would otherwise occur at module load time.

[gemini-code-assist]

The warning message hardcodes ~/.genie/config.json, which may be inaccurate if the GENIE_HOME environment variable is set. It's better to dynamically resolve the config path to provide accurate guidance to the user.

Suggested change

	console.warn(' Agent sync: DISABLED — no workspace found from cwd or ~/.genie/config.json');
	console.warn(" Agent sync: DISABLED — no workspace found from cwd or " + join(genieHome(), 'config.json'));