- Add stability-based completion detection (10s min + 3 stable polls)
- Fix message extraction to recognize 'reasoning' parts from thinking models
- Switch from promptAsync() to prompt() for proper agent initialization
- Remove model parameter from prompt body (use agent's configured model)
- Add fire-and-forget prompt pattern for sisyphus_task sync mode
- Add silent notification via tool.execute.after hook injection
- Fix indentation issues in manager.ts and index.ts

Incorporates fixes from:
- PR code-yeongyu#592: Stability detection mechanism
- PR code-yeongyu#610: Model parameter passing (partially)
- PR code-yeongyu#628: Completion detection improvements

Known limitation: Thinking models (e.g. claude-*-thinking-*) cause
JSON Parse errors in child sessions. Use non-thinking models for
background agents until OpenCode core resolves this.

…ion (#638)

* fix: background task completion detection and silent notifications

- Fix TS2742 by adding explicit ToolDefinition type annotations
- Add stability detection (3 consecutive stable polls after 10s minimum)
- Remove early continue when sessionStatus is undefined
- Add silent notification system via tool.execute.after hook injection
- Change task retention from 200ms to 5 minutes for background_output retrieval
- Fix formatTaskResult to sort messages by time descending

Fixes hanging background tasks that never complete due to missing sessionStatus.

* fix: improve background task completion detection and message extraction

- Add stability-based completion detection (10s min + 3 stable polls)
- Fix message extraction to recognize 'reasoning' parts from thinking models
- Switch from promptAsync() to prompt() for proper agent initialization
- Remove model parameter from prompt body (use agent's configured model)
- Add fire-and-forget prompt pattern for sisyphus_task sync mode
- Add silent notification via tool.execute.after hook injection
- Fix indentation issues in manager.ts and index.ts

Incorporates fixes from:
- PR #592: Stability detection mechanism
- PR #610: Model parameter passing (partially)
- PR #628: Completion detection improvements

Known limitation: Thinking models (e.g. claude-*-thinking-*) cause
JSON Parse errors in child sessions. Use non-thinking models for
background agents until OpenCode core resolves this.

* fix: add tool_result handling and pendingByParent tracking for resume/external tasks

Addresses code review feedback from PR #638:

P1: Add tool_result type to validateSessionHasOutput() to prevent
    false negatives for tool-only background tasks that would otherwise
    timeout after 30 minutes despite having valid results.

P2: Add pendingByParent tracking to resume() and registerExternalTask()
    to prevent premature 'ALL COMPLETE' notifications when mixing
    launched and resumed tasks.

* fix: address code review feedback - log messages, model passthrough, sorting, race condition

- Fix misleading log messages: 'promptAsync' -> 'prompt (fire-and-forget)'
- Restore model passthrough in launch() for Sisyphus category configs
- Fix call-omo-agent sorting: use time.created number instead of String(time)
- Fix race condition: check promptError inside polling loop, not just after 100ms

…ing and sync mode

## Summary

This commit represents the culmination of extensive debugging and refinement
of the background agent and sisyphus_task systems, building upon changes from
PRs code-yeongyu#592, code-yeongyu#610, code-yeongyu#628, code-yeongyu#638, code-yeongyu#648, code-yeongyu#649, code-yeongyu#652, and code-yeongyu#653.

## Investigation Journey

### Initial Problem
Background tasks were getting stuck indefinitely. User config model overrides
were being ignored for certain agent types.

### Root Cause Analysis
1. Discovered validateSessionHasOutput and checkSessionTodos guards were
   blocking completion even when tasks had finished
2. Found that sync mode (run_in_background=false) was NOT passing categoryModel
   to session.prompt(), while async mode was
3. Traced config loading path and found JSONC files weren't being detected
4. Analyzed kdcokenny/opencode-background-agents for reference implementation

### Trial and Error Log

**Attempt 1: Add model to resume() in manager.ts**
- Hypothesis: Resume needs to pass stored model
- Result: REVERTED - PR code-yeongyu#638 intentionally removed this; agent config handles it

**Attempt 2: Add userAgents lookup for subagent_type**
- Hypothesis: Need to look up agent model from user config
- Result: REVERTED - Agent model already applied at creation in config-handler.ts

**Attempt 3: Add categoryModel to sync mode prompt**
- Hypothesis: Sync mode missing model that async mode passes
- Result: SUCCESS - This was the actual bug

**Attempt 4: Add debug logging throughout pipeline**
- Purpose: Trace model flow through config -> agent -> prompt
- Files: 6 files with appendFileSync to omo-debug.log
- Result: Confirmed fixes working, then REMOVED all debug logging

**Attempt 5: Investigate clickable sessions**
- Hypothesis: parentID should make child sessions clickable in UI
- Result: parentID IS passed correctly, but sessions don't appear clickable
- Analysis: kdcokenny uses same approach; may be OpenCode core limitation
- Status: UNRESOLVED - Needs further investigation or OpenCode core change

## Background Agent Completion Detection (PR code-yeongyu#638)

Simplified the completion detection logic that was causing tasks to get stuck:
- Removed overly complex validateSessionHasOutput and checkSessionTodos guards
- Tasks now complete after MIN_IDLE_TIME_MS (5s) elapsed on session.idle event
- Added 15-minute global timeout (MAX_RUN_TIME_MS) to prevent runaway tasks
- Pattern follows kdcokenny/opencode-background-agents reference implementation

## Model Override Architecture (PRs code-yeongyu#610, code-yeongyu#628, code-yeongyu#638)

Established clear separation between category-based and agent-based model handling:

| Path              | Model Source                              |
|-------------------|-------------------------------------------|
| category=X        | Explicit from category config (passed)    |
| subagent_type=X   | Agent's configured model (at creation)    |
| resume            | Agent's configured model (not passed)     |

Key insight from PR code-yeongyu#638: Don't pass model in prompt body for resume/subagent -
let OpenCode use the agent's configured model set at creation time in
config-handler.ts.

## Sync Mode Category Model Fix (NEW)

Fixed critical bug where sync mode (run_in_background=false) with categories
was NOT passing the categoryModel to session.prompt():

  // BEFORE: Model not passed in sync mode
  body: { agent: agentToUse, system: systemContent, ... }

  // AFTER: Model passed when available
  body: { agent: agentToUse, ...(categoryModel ? { model: categoryModel } : {}), ... }

This ensures category model overrides work consistently in both sync and async modes.

## JSONC Config File Support

Extended config file detection to support both .json and .jsonc extensions:
- getUserConfigDir() now checks for oh-my-opencode.jsonc first
- Both cross-platform (~/.config) and Windows (%APPDATA%) paths support JSONC
- Enables comments in config files for better documentation

## Test Improvements

- Increased sync resume test timeout from 5s to 10s
- Test was flaky because timeout = MIN_STABILITY_TIME_MS (race condition)
- Added clarifying comments about timing requirements

## Code Cleanup

- Removed unused 'os' imports from plugin-config.ts and config-handler.ts
- Removed ALL debug logging (hardcoded paths, appendFileSync calls)
- Added PR code-yeongyu#638 reference comments for future maintainers

## Verified Test Results (8/8 category + subagent tests pass)

| Test              | Type        | Mode  | Result |
|-------------------|-------------|-------|--------|
| quick             | category    | async | ✅     |
| ultrabrain        | category    | async | ✅     |
| most-capable      | category    | async | ✅     |
| quick             | category    | sync  | ✅     |
| librarian         | subagent    | async | ✅     |
| Metis             | subagent    | async | ✅     |
| oracle            | subagent    | sync  | ✅     |
| quick + git-master| category    | async | ✅     |

## Known Issues & Future Work

### 1. Explore Agent Hangs on Non-Exploration Tasks
The explore agent hung when given a simple math query (5+5). This is NOT a
regression - explore is a specialized codebase search agent (contextual grep)
designed for queries like 'Where is X implemented?' not general Q&A.

When given non-exploration tasks, it attempts to search for non-existent
patterns and may hang indefinitely due to no max_steps limit.

**Recommendation**: Add max_steps: 10 to explore agent config in future PR.

### 2. Clickable Child Sessions Not Working
Sessions created via sisyphus_task pass parentID correctly, but don't appear
as clickable child sessions in OpenCode's sidebar UI. Investigation showed:
- parentID IS being passed to session.create()
- kdcokenny/opencode-background-agents uses identical approach
- Sessions exist and complete, just not rendered as clickable in UI

**Recommendation**: May require OpenCode core change or UI setting discovery.

### 3. Prometheus Agent Correctly Blocked
Prometheus (Planner) is a primary agent and correctly rejected when called
via sisyphus_task with subagent_type. This is expected behavior - primary
agents should only be invoked directly, not via task delegation.

## Files Changed

- src/features/background-agent/manager.ts - PR code-yeongyu#638 reference comment
- src/tools/sisyphus-task/tools.ts - Sync mode categoryModel fix
- src/tools/sisyphus-task/tools.test.ts - Test timeout increase
- src/shared/config-path.ts - JSONC extension support
- src/plugin-config.ts - Cleanup unused import
- src/plugin-handlers/config-handler.ts - Cleanup unused import

- Add stability-based completion detection (10s min + 3 stable polls)
- Fix message extraction to recognize 'reasoning' parts from thinking models
- Switch from promptAsync() to prompt() for proper agent initialization
- Remove model parameter from prompt body (use agent's configured model)
- Add fire-and-forget prompt pattern for sisyphus_task sync mode
- Add silent notification via tool.execute.after hook injection
- Fix indentation issues in manager.ts and index.ts

Incorporates fixes from:
- PR code-yeongyu#592: Stability detection mechanism
- PR code-yeongyu#610: Model parameter passing (partially)
- PR code-yeongyu#628: Completion detection improvements

Known limitation: Thinking models (e.g. claude-*-thinking-*) cause
JSON Parse errors in child sessions. Use non-thinking models for
background agents until OpenCode core resolves this.