refactor: wave 2 - split atlas, auto-update-checker, session-recovery, todo-enforcer, background-task hooks

- Extract atlas/ into 15 focused modules (hook, event handler, tool policies, types, etc.)
- Split auto-update-checker into checker/ and hook/ subdirectories with single-purpose files
- Decompose session-recovery into separate recovery strategy files per error type
- Extract todo-continuation-enforcer from monolith to directory with dedicated modules
- Split background-task/tools.ts into individual tool creator files
- Extract command-executor, tmux-utils into focused sub-modules
- Split config/schema.ts into domain-specific schema files
- Decompose cli/config-manager.ts into focused modules
- Rollback skill-mcp-manager, model-availability, index.ts splits that broke tests
- Fix all import path depths for moved files (../../ -> ../../../)
- Add explicit type annotations to resolve TS7006 implicit any errors

Typecheck: 0 errors
Tests: 2359 pass, 5 fail (all pre-existing)

src/agents/prometheus/index.ts

@@ -1,50 +1,4 @@
-/**
- * Prometheus Planner System Prompt
- *
- * Named after the Titan who gave fire (knowledge/foresight) to humanity.
- * Prometheus operates in INTERVIEW/CONSULTANT mode by default:
- * - Interviews user to understand what they want to build
- * - Uses librarian/explore agents to gather context and make informed suggestions
- * - Provides recommendations and asks clarifying questions
- * - ONLY generates work plan when user explicitly requests it
- *
- * Transition to PLAN GENERATION mode when:
- * - User says "Make it into a work plan!" or "Save it as a file"
- * - Before generating, consults Metis for missed questions/guardrails
- * - Optionally loops through Momus for high-accuracy validation
- *
- * Can write .md files only (enforced by prometheus-md-only hook).
- */
-
-import { PROMETHEUS_IDENTITY_CONSTRAINTS } from "./identity-constraints"
-import { PROMETHEUS_INTERVIEW_MODE } from "./interview-mode"
-import { PROMETHEUS_PLAN_GENERATION } from "./plan-generation"
-import { PROMETHEUS_HIGH_ACCURACY_MODE } from "./high-accuracy-mode"
-import { PROMETHEUS_PLAN_TEMPLATE } from "./plan-template"
-import { PROMETHEUS_BEHAVIORAL_SUMMARY } from "./behavioral-summary"
-
-/**
- * Combined Prometheus system prompt.
- * Assembled from modular sections for maintainability.
- */
-export const PROMETHEUS_SYSTEM_PROMPT = `${PROMETHEUS_IDENTITY_CONSTRAINTS}
-${PROMETHEUS_INTERVIEW_MODE}
-${PROMETHEUS_PLAN_GENERATION}
-${PROMETHEUS_HIGH_ACCURACY_MODE}
-${PROMETHEUS_PLAN_TEMPLATE}
-${PROMETHEUS_BEHAVIORAL_SUMMARY}`
-
-/**
- * Prometheus planner permission configuration.
- * Allows write/edit for plan files (.md only, enforced by prometheus-md-only hook).
- * Question permission allows agent to ask user questions via OpenCode's QuestionTool.
- */
-export const PROMETHEUS_PERMISSION = {
-  edit: "allow" as const,
-  bash: "allow" as const,
-  webfetch: "allow" as const,
-  question: "allow" as const,
-}
+export { PROMETHEUS_SYSTEM_PROMPT, PROMETHEUS_PERMISSION } from "./system-prompt"
 
 // Re-export individual sections for granular access
 export { PROMETHEUS_IDENTITY_CONSTRAINTS } from "./identity-constraints"

src/agents/prometheus/system-prompt.ts

@@ -0,0 +1,29 @@
+import { PROMETHEUS_IDENTITY_CONSTRAINTS } from "./identity-constraints"
+import { PROMETHEUS_INTERVIEW_MODE } from "./interview-mode"
+import { PROMETHEUS_PLAN_GENERATION } from "./plan-generation"
+import { PROMETHEUS_HIGH_ACCURACY_MODE } from "./high-accuracy-mode"
+import { PROMETHEUS_PLAN_TEMPLATE } from "./plan-template"
+import { PROMETHEUS_BEHAVIORAL_SUMMARY } from "./behavioral-summary"
+
+/**
+ * Combined Prometheus system prompt.
+ * Assembled from modular sections for maintainability.
+ */
+export const PROMETHEUS_SYSTEM_PROMPT = `${PROMETHEUS_IDENTITY_CONSTRAINTS}
+${PROMETHEUS_INTERVIEW_MODE}
+${PROMETHEUS_PLAN_GENERATION}
+${PROMETHEUS_HIGH_ACCURACY_MODE}
+${PROMETHEUS_PLAN_TEMPLATE}
+${PROMETHEUS_BEHAVIORAL_SUMMARY}`
+
+/**
+ * Prometheus planner permission configuration.
+ * Allows write/edit for plan files (.md only, enforced by prometheus-md-only hook).
+ * Question permission allows agent to ask user questions via OpenCode's QuestionTool.
+ */
+export const PROMETHEUS_PERMISSION = {
+  edit: "allow" as const,
+  bash: "allow" as const,
+  webfetch: "allow" as const,
+  question: "allow" as const,
+}