diff --git a/src/cli.ts b/src/cli.ts
index 342cb9674..97ed54a79 100644
--- a/src/cli.ts
+++ b/src/cli.ts
@@ -8,7 +8,7 @@ import {
   InteractiveMode,
   runPrintMode,
 } from '@mariozechner/pi-coding-agent'
-import { readFileSync } from 'node:fs'
+import { existsSync, readdirSync, renameSync, readFileSync } from 'node:fs'
 import { join } from 'node:path'
 import { agentDir, sessionsDir, authFilePath } from './app-paths.js'
 import { initResources } from './resource-loader.js'
@@ -180,6 +180,30 @@ if (isPrintMode) {
 const cwd = process.cwd()
 const safePath = `--${cwd.replace(/^[/\\]/, '').replace(/[/\\:]/g, '-')}--`
 const projectSessionsDir = join(sessionsDir, safePath)
+
+// Migrate legacy flat sessions: before per-directory scoping, all .jsonl session
+// files lived directly in ~/.gsd/sessions/. Move them into the correct per-cwd
+// subdirectory so /resume can find them.
+if (existsSync(sessionsDir)) {
+  try {
+    const entries = readdirSync(sessionsDir)
+    const flatJsonl = entries.filter(f => f.endsWith('.jsonl'))
+    if (flatJsonl.length > 0) {
+      const { mkdirSync } = await import('node:fs')
+      mkdirSync(projectSessionsDir, { recursive: true })
+      for (const file of flatJsonl) {
+        const src = join(sessionsDir, file)
+        const dst = join(projectSessionsDir, file)
+        if (!existsSync(dst)) {
+          renameSync(src, dst)
+        }
+      }
+    }
+  } catch {
+    // Non-fatal — don't block startup if migration fails
+  }
+}
+
 const sessionManager = SessionManager.create(cwd, projectSessionsDir)
 
 initResources(agentDir)
diff --git a/src/resources/extensions/gsd/worktree.ts b/src/resources/extensions/gsd/worktree.ts
index 36c153f7c..450ffc586 100644
--- a/src/resources/extensions/gsd/worktree.ts
+++ b/src/resources/extensions/gsd/worktree.ts
@@ -86,6 +86,17 @@ export function ensureSliceBranch(basePath: string, milestoneId: string, sliceId
     created = true;
   }
 
+  // Auto-commit dirty files before checkout to prevent "would be overwritten" errors.
+  // This handles cases where doctor, STATE.md rebuild, or agent work left uncommitted changes.
+  const status = runGit(basePath, ["status", "--short"]);
+  if (status.trim()) {
+    runGit(basePath, ["add", "-A"]);
+    const staged = runGit(basePath, ["diff", "--cached", "--stat"]);
+    if (staged.trim()) {
+      runGit(basePath, ["commit", "-m", `"chore: auto-commit before switching to ${branch}"`]);
+    }
+  }
+
   runGit(basePath, ["checkout", branch]);
   return created;
 }