fix(coding-agent): delete empty draft sessions on shutdown and sweep ghosts at startup

[ruttybob]

Closes #1078

Problem

Empty session files (ghost sessions) accumulate in ~/.prime/agent/sessions/ after every daemon shutdown or update restart. These files contain zero messages — only the 4 bootstrap entries plus a daemon-written session_state:active (~768 bytes). Orphaned session-lease directories also accumulate when a daemon exits without releasing its lease. Neither is ever cleaned up.

Full diagnosis and evidence in #1078.

Root cause

Two layers:

1. Ghost creation (now fixed)

SessionManager._persist() allowed session_state entries to bypass the "no assistant message → don't write to disk" guard:

// Before:
const shouldPersistWithoutAssistant = entry.type === "session_state" || entry.type === "session_info";

When addRuntime() calls appendSessionState({ status: "active" }), _persist wrote the file immediately — before any user message. This is the ghost's birth.

// After:
const shouldPersistWithoutAssistant = entry.type === "session_info";

session_info bypass is kept so explicit /name renames persist immediately. The file is now created only when the first assistant message triggers _rewriteFile, which writes all accumulated entries (including the deferred session_state) at once.

2. Ghost persistence (original PR #1079 fix)

closeSessionOnce() gated isEmptyDraftSession on closeKeepsResumeEntry(reason):

const keepsResumeEntry = this.closeKeepsResumeEntry(reason);          // true for "shutdown" | "update"
const isEmptyDraftSession = !keepsResumeEntry && this.isEmptyDraftContent(state);
//                     ↑ ALWAYS FALSE for shutdown/update

For shutdown/update, keepsResumeEntry is true → isEmptyDraftSession is always false → deleteSessionFile() is never called. The empty draft stays on disk permanently.

Fix

Root cause prevention (commit df9959a)

Remove session_state from the _persist bypass so ghost files are never created in the first place.

Cleanup at close (commit 153b291)

Replace the keepsResumeEntry gate with isActiveSessionBusy — mirroring the existing isDiscardableDraft() in the detach-time discard path:

// Before:
const isEmptyDraftSession = !keepsResumeEntry && this.isEmptyDraftContent(state);

// After:
const isEmptyDraftSession = this.isEmptyDraftContent(state) && !isActiveSessionBusy(state);

Empty drafts are now deleted on all close reasons, but only when the session is truly idle (not streaming, not compacting, no unfinished actions, no running subagents). keepsResumeEntry still gates archiving and error propagation unchanged.

Safety nets

Change	What
sweepStaleSessionLeases(agentDir) in session-lease.ts	At daemon startup, remove lease directories whose owner PID is dead
sweepGhostSessionFiles(sessionDir) in session-file-actions.ts	At daemon startup, remove session files containing only bootstrap entries + session_state
sweepStaleStartupState() in daemon-mode.ts start()	Fires both sweeps — best-effort, fire-and-forget, never blocks startup

Consumer safety (verified — root cause fix is safe)

All 5 places that read state.status from disk were verified safe after removing session_state from the _persist bypass:

Consumer	Reads	Safe because
inactiveLifecycleForSession	status === "archived"	Only reads EXISTING files — which now always have an assistant message
isPersistedCronJobRunnable	status !== "active"	Cron jobs can only be created on sessions with user interaction → file already exists
restoreRlmHeartbeatSession	parentInfo.state?.status	Parent restored via createRuntime → "active" re-written
archiveSession	Writes "archived"	Only called for non-empty sessions
deactivatePendingAgent	Writes "archived"	Checks existsSync(sessionFile) before opening

Tests (9 new, all green)

File	Test
session-manager-flush.test.ts	appendSessionState(active) does NOT create a file before assistant message
session-manager-flush.test.ts	After first assistant message, file IS created and INCLUDES session_state entry
daemon-mode.test.ts	Empty draft + shutdown → file deleted
daemon-mode.test.ts	Session with user content + shutdown → file preserved
daemon-mode.test.ts	2 existing mock tests updated with hasRunningRlmChildren
session-lease.test.ts	Stale lease swept, live lease preserved
session-lease.test.ts	Missing directory → 0
session-artifacts-delete.test.ts	Ghost file removed, real session preserved
session-artifacts-delete.test.ts	Missing directory → 0

Checklist

• Typecheck (tsgo --noEmit) passes
• Biome lint/format passes
• Pre-commit hooks pass (biome + typecheck + installer + browser smoke)
• No new dependencies

[kevinjosethomas]

Hi, thanks for taking the time to contribute to Prime Agent! Since open sourcing the project, we’ve received far more pull requests than we can responsibly review and validate. Prime Agent runs directly on users’ machines, so we need to be deliberate about which changes we accept and how they are reviewed. Rather than leave a large backlog that we cannot meaningfully work through, we’re closing the current PR queue and moving to a discussion-first contribution process.

We have established new contribution guidelines to help us continue iterating on Prime Agent and better manage contributions from the community. Going forward, we won’t review unsolicited pull requests. Instead, please start with a GitHub Discussion. We’ll identify recurring bugs and feature requests, create Issues for work we want to pursue, and invite pull requests from maintainers or vouched contributors when implementation is ready. Please read the full process documented in our contribution guidelines.

While we’re closing this backlog, we’re still reviewing it at a high level to identify recurring bugs, useful ideas, and important problems that we should address ourselves. Thanks again for the time you put into this!