merge: integrate origin/dev into modular-enforcement branch

Resolves all merge conflicts, preserving our split module structure
while integrating all dev changes:
- Custom agent summaries support (parseRegisteredAgentSummaries)
- Background notification queue (enqueueNotificationForParent)
- Atlas shared git-worktree module (collectGitDiffStats, formatFileChanges)
- Ralph-loop withTimeout + DEFAULT_API_TIMEOUT=5000
- Session recovery assistant_prefill_unsupported error type
- Atlas agentOverrides forwarding
- Config handler plan model demotion (buildPlanDemoteConfig)
- Delegate-task agentOverrides, promptSyncWithModelSuggestionRetry, variant
- LSP init timeout + stale init detection
- isPlanFamily function + task-continuation-enforcer hook
- Handoff command

src/hooks/atlas/git-diff-stats.ts

@@ -1,133 +0,0 @@
-import { execSync } from "node:child_process"
-
-interface GitFileStat {
-  path: string
-  added: number
-  removed: number
-  status: "modified" | "added" | "deleted"
-}
-
-export function getGitDiffStats(directory: string): GitFileStat[] {
-  try {
-    const statusOutput = execSync("git status --porcelain", {
-      cwd: directory,
-      encoding: "utf-8",
-      timeout: 5000,
-      stdio: ["pipe", "pipe", "pipe"],
-    }).trim()
-
-    if (!statusOutput) return []
-
-    const statusMap = new Map<string, "modified" | "added" | "deleted">()
-    const untrackedFiles: string[] = []
-    for (const line of statusOutput.split("\n")) {
-      if (!line) continue
-      const status = line.substring(0, 2).trim()
-      const filePath = line.substring(3)
-      if (status === "??") {
-        statusMap.set(filePath, "added")
-        untrackedFiles.push(filePath)
-      } else if (status === "A") {
-        statusMap.set(filePath, "added")
-      } else if (status === "D") {
-        statusMap.set(filePath, "deleted")
-      } else {
-        statusMap.set(filePath, "modified")
-      }
-    }
-
-    const output = execSync("git diff --numstat HEAD", {
-      cwd: directory,
-      encoding: "utf-8",
-      timeout: 5000,
-      stdio: ["pipe", "pipe", "pipe"],
-    }).trim()
-
-    const stats: GitFileStat[] = []
-    const trackedPaths = new Set<string>()
-
-    if (output) {
-      for (const line of output.split("\n")) {
-        const parts = line.split("\t")
-        if (parts.length < 3) continue
-
-        const [addedStr, removedStr, path] = parts
-        const added = addedStr === "-" ? 0 : parseInt(addedStr, 10)
-        const removed = removedStr === "-" ? 0 : parseInt(removedStr, 10)
-        trackedPaths.add(path)
-
-        stats.push({
-          path,
-          added,
-          removed,
-          status: statusMap.get(path) ?? "modified",
-        })
-      }
-    }
-
-    for (const filePath of untrackedFiles) {
-      if (trackedPaths.has(filePath)) continue
-      try {
-        const content = execSync(`wc -l < "${filePath}"`, {
-          cwd: directory,
-          encoding: "utf-8",
-          timeout: 3000,
-          stdio: ["pipe", "pipe", "pipe"],
-        }).trim()
-        const lineCount = parseInt(content, 10) || 0
-        stats.push({ path: filePath, added: lineCount, removed: 0, status: "added" })
-      } catch {
-        stats.push({ path: filePath, added: 0, removed: 0, status: "added" })
-      }
-    }
-
-    return stats
-  } catch {
-    return []
-  }
-}
-
-export function formatFileChanges(stats: GitFileStat[], notepadPath?: string): string {
-  if (stats.length === 0) return "[FILE CHANGES SUMMARY]\nNo file changes detected.\n"
-
-  const modified = stats.filter((s) => s.status === "modified")
-  const added = stats.filter((s) => s.status === "added")
-  const deleted = stats.filter((s) => s.status === "deleted")
-
-  const lines: string[] = ["[FILE CHANGES SUMMARY]"]
-
-  if (modified.length > 0) {
-    lines.push("Modified files:")
-    for (const f of modified) {
-      lines.push(`  ${f.path}  (+${f.added}, -${f.removed})`)
-    }
-    lines.push("")
-  }
-
-  if (added.length > 0) {
-    lines.push("Created files:")
-    for (const f of added) {
-      lines.push(`  ${f.path}  (+${f.added})`)
-    }
-    lines.push("")
-  }
-
-  if (deleted.length > 0) {
-    lines.push("Deleted files:")
-    for (const f of deleted) {
-      lines.push(`  ${f.path}  (-${f.removed})`)
-    }
-    lines.push("")
-  }
-
-  if (notepadPath) {
-    const notepadStat = stats.find((s) => s.path.includes("notepad") || s.path.includes(".sisyphus"))
-    if (notepadStat) {
-      lines.push("[NOTEPAD UPDATED]")
-      lines.push(`  ${notepadStat.path}  (+${notepadStat.added})`)
-      lines.push("")
-    }
-  }
-
-  return lines.join("\n")
-}

src/hooks/atlas/tool-execute-after.ts

@@ -2,9 +2,9 @@ import type { PluginInput } from "@opencode-ai/plugin"
 import { appendSessionId, getPlanProgress, readBoulderState } from "../../features/boulder-state"
 import { log } from "../../shared/logger"
 import { isCallerOrchestrator } from "../../shared/session-utils"
+import { collectGitDiffStats, formatFileChanges } from "../../shared/git-worktree"
 import { HOOK_NAME } from "./hook-name"
 import { DIRECT_WORK_REMINDER } from "./system-reminder-templates"
-import { formatFileChanges, getGitDiffStats } from "./git-diff-stats"
 import { isSisyphusPath } from "./sisyphus-path"
 import { extractSessionIdFromOutput } from "./subagent-session-id"
 import { buildOrchestratorReminder, buildStandaloneVerificationReminder } from "./verification-reminders"
@@ -57,7 +57,7 @@ export function createToolExecuteAfterHandler(input: {
     }
 
     if (toolOutput.output && typeof toolOutput.output === "string") {
-      const gitStats = getGitDiffStats(ctx.directory)
+      const gitStats = collectGitDiffStats(ctx.directory)
       const fileChanges = formatFileChanges(gitStats)
       const subagentSessionId = extractSessionIdFromOutput(toolOutput.output)
 

src/hooks/atlas/types.ts

@@ -1,3 +1,4 @@
+import type { AgentOverrides } from "../../config"
 import type { BackgroundManager } from "../../features/background-agent"
 
 export type ModelInfo = { providerID: string; modelID: string }
@@ -6,6 +7,7 @@ export interface AtlasHookOptions {
   directory: string
   backgroundManager?: BackgroundManager
   isContinuationStopped?: (sessionID: string) => boolean
+  agentOverrides?: AgentOverrides
 }
 
 export interface ToolExecuteAfterInput {