diff --git a/packages/app/src/components/grouped-agent-list.tsx b/packages/app/src/components/grouped-agent-list.tsx
index 94c15eb4c..510b5b101 100644
--- a/packages/app/src/components/grouped-agent-list.tsx
+++ b/packages/app/src/components/grouped-agent-list.tsx
@@ -121,14 +121,17 @@ function SectionHeader({
     }
   }
 
+  const createAgentWorkingDir =
+    (checkout?.isPaseoOwnedWorktree ? checkout.mainRepoRoot : null) ?? section.workingDir;
+
   const handleCreatePress = useCallback(
     (e: { stopPropagation: () => void }) => {
       e.stopPropagation();
-      if (section.workingDir) {
-        onCreateAgent(section.workingDir);
+      if (createAgentWorkingDir) {
+        onCreateAgent(createAgentWorkingDir);
       }
     },
-    [onCreateAgent, section.workingDir]
+    [onCreateAgent, createAgentWorkingDir]
   );
 
   return (
@@ -171,7 +174,7 @@ function SectionHeader({
         </Text>
       </View>
       <View style={styles.sectionHeaderRight}>
-        {section.workingDir && (
+        {createAgentWorkingDir && (
           <Pressable
             style={styles.createAgentButton}
             onPress={handleCreatePress}
diff --git a/packages/server/src/server/agent/providers/claude-agent.test.ts b/packages/server/src/server/agent/providers/claude-agent.test.ts
index 782d13195..f2dbf64b6 100644
--- a/packages/server/src/server/agent/providers/claude-agent.test.ts
+++ b/packages/server/src/server/agent/providers/claude-agent.test.ts
@@ -1218,7 +1218,8 @@ function assertHydratedReplica(
 }
 
 function sanitizeClaudeProjectName(cwd: string): string {
-  return cwd.replace(/[\\/]/g, "-").replace(/_/g, "-");
+  // Match Claude CLI's path sanitization: replace slashes, dots, and underscores with dashes
+  return cwd.replace(/[\\/\.]/g, "-").replace(/_/g, "-");
 }
 
 function resolveClaudeHistoryPath(cwd: string, sessionId: string): string {
diff --git a/packages/server/src/server/agent/providers/claude-agent.ts b/packages/server/src/server/agent/providers/claude-agent.ts
index b2dec4a2b..f3ad25eae 100644
--- a/packages/server/src/server/agent/providers/claude-agent.ts
+++ b/packages/server/src/server/agent/providers/claude-agent.ts
@@ -1260,7 +1260,8 @@ class ClaudeAgentSession implements AgentSession {
   private resolveHistoryPath(sessionId: string): string | null {
     const cwd = this.config.cwd;
     if (!cwd) return null;
-    const sanitized = cwd.replace(/[\\/]/g, "-").replace(/_/g, "-");
+    // Match Claude CLI's path sanitization: replace slashes, dots, and underscores with dashes
+    const sanitized = cwd.replace(/[\\/\.]/g, "-").replace(/_/g, "-");
     const configDir = process.env.CLAUDE_CONFIG_DIR ?? path.join(os.homedir(), ".claude");
     const dir = path.join(configDir, "projects", sanitized);
     return path.join(dir, `${sessionId}.jsonl`);
diff --git a/packages/server/src/server/session.ts b/packages/server/src/server/session.ts
index 38abeb9cc..965788382 100644
--- a/packages/server/src/server/session.ts
+++ b/packages/server/src/server/session.ts
@@ -2503,6 +2503,7 @@ export class Session {
             cwd,
             isGit: true,
             repoRoot: status.repoRoot ?? null,
+            mainRepoRoot: status.mainRepoRoot,
             currentBranch: status.currentBranch ?? null,
             isDirty: status.isDirty ?? null,
             baseRef: status.baseRef,
diff --git a/packages/server/src/shared/messages.ts b/packages/server/src/shared/messages.ts
index b7042ba4b..ac802ad4b 100644
--- a/packages/server/src/shared/messages.ts
+++ b/packages/server/src/shared/messages.ts
@@ -1124,6 +1124,7 @@ const CheckoutStatusGitPaseoSchema = CheckoutStatusCommonSchema.extend({
   isGit: z.literal(true),
   isPaseoOwnedWorktree: z.literal(true),
   repoRoot: z.string(),
+  mainRepoRoot: z.string(),
   currentBranch: z.string().nullable(),
   isDirty: z.boolean(),
   baseRef: z.string(),
diff --git a/packages/server/src/utils/checkout-git.test.ts b/packages/server/src/utils/checkout-git.test.ts
index f645928e6..7d30a074e 100644
--- a/packages/server/src/utils/checkout-git.test.ts
+++ b/packages/server/src/utils/checkout-git.test.ts
@@ -117,6 +117,8 @@ describe("checkout git utilities", () => {
     expect(status.isGit).toBe(true);
     expect(status.repoRoot).toBe(result.worktreePath);
     expect(status.isDirty).toBe(true);
+    expect(status.isPaseoOwnedWorktree).toBe(true);
+    expect(status.mainRepoRoot).toBe(repoDir);
 
     const diff = await getCheckoutDiff(result.worktreePath, { mode: "uncommitted" }, { paseoHome });
     expect(diff.diff).toContain("-hello");
@@ -134,6 +136,29 @@ describe("checkout git utilities", () => {
     expect(message).toBe("worktree update");
   });
 
+  it("returns mainRepoRoot pointing to first non-bare worktree for bare repos", async () => {
+    const bareRepoDir = join(tempDir, "bare-repo");
+    execSync(`git clone --bare ${repoDir} ${bareRepoDir}`);
+
+    const mainCheckoutDir = join(tempDir, "main-checkout");
+    execSync(`git -C ${bareRepoDir} worktree add ${mainCheckoutDir} main`);
+    execSync("git config user.email 'test@test.com'", { cwd: mainCheckoutDir });
+    execSync("git config user.name 'Test'", { cwd: mainCheckoutDir });
+
+    const worktree = await createWorktree({
+      branchName: "feature",
+      cwd: mainCheckoutDir,
+      baseBranch: "main",
+      worktreeSlug: "feature-worktree",
+      paseoHome,
+    });
+
+    const status = await getCheckoutStatus(worktree.worktreePath, { paseoHome });
+    expect(status.isGit).toBe(true);
+    expect(status.isPaseoOwnedWorktree).toBe(true);
+    expect(status.mainRepoRoot).toBe(mainCheckoutDir);
+  });
+
   it("merges the current branch into base from a worktree checkout", async () => {
     const worktree = await createWorktree({
       branchName: "main",
diff --git a/packages/server/src/utils/checkout-git.ts b/packages/server/src/utils/checkout-git.ts
index 6ddd9a2ba..8db383f24 100644
--- a/packages/server/src/utils/checkout-git.ts
+++ b/packages/server/src/utils/checkout-git.ts
@@ -1,6 +1,7 @@
 import { exec, execFile } from "child_process";
 import { promisify } from "util";
-import { resolve } from "path";
+import { resolve, dirname, basename } from "path";
+import { realpathSync } from "fs";
 import type { ParsedDiffFile } from "../server/utils/diff-highlighter.js";
 import { parseAndHighlightDiff } from "../server/utils/diff-highlighter.js";
 import { isPaseoOwnedWorktreeCwd } from "./worktree.js";
@@ -79,6 +80,7 @@ export type CheckoutStatusGitNonPaseo = {
 export type CheckoutStatusGitPaseo = {
   isGit: true;
   repoRoot: string;
+  mainRepoRoot: string;
   currentBranch: string | null;
   isDirty: boolean;
   baseRef: string;
@@ -156,9 +158,37 @@ async function getWorktreeRoot(cwd: string): Promise<string | null> {
   }
 }
 
+async function getMainRepoRoot(cwd: string): Promise<string> {
+  const { stdout: commonDirOut } = await execAsync(
+    "git rev-parse --path-format=absolute --git-common-dir",
+    { cwd, env: READ_ONLY_GIT_ENV }
+  );
+  const commonDir = commonDirOut.trim();
+  const normalized = realpathSync(commonDir);
+
+  if (basename(normalized) === ".git") {
+    return dirname(normalized);
+  }
+
+  const { stdout: worktreeOut } = await execAsync("git worktree list --porcelain", {
+    cwd,
+    env: READ_ONLY_GIT_ENV,
+  });
+  const worktrees = parseWorktreeList(worktreeOut);
+  const nonBareNonPaseo = worktrees.filter(
+    (wt) => !wt.isBare && !wt.path.includes("/.paseo/worktrees/")
+  );
+  const childrenOfBareRepo = nonBareNonPaseo.filter((wt) =>
+    wt.path.startsWith(normalized + "/")
+  );
+  const mainChild = childrenOfBareRepo.find((wt) => basename(wt.path) === "main");
+  return mainChild?.path ?? childrenOfBareRepo[0]?.path ?? nonBareNonPaseo[0]?.path ?? normalized;
+}
+
 type GitWorktreeEntry = {
   path: string;
   branchRef?: string;
+  isBare?: boolean;
 };
 
 function parseWorktreeList(output: string): GitWorktreeEntry[] {
@@ -179,6 +209,9 @@ function parseWorktreeList(output: string): GitWorktreeEntry[] {
     if (current && trimmed.startsWith("branch ")) {
       current.branchRef = trimmed.slice("branch ".length).trim();
     }
+    if (current && trimmed === "bare") {
+      current.isBare = true;
+    }
   }
   if (current) {
     entries.push(current);
@@ -460,9 +493,11 @@ export async function getCheckoutStatus(
     hasRemote && currentBranch ? await getAheadOfOrigin(cwd, currentBranch) : null;
 
   if (configured.isPaseoOwnedWorktree) {
+    const mainRepoRoot = await getMainRepoRoot(cwd);
     return {
       isGit: true,
       repoRoot: worktreeRoot,
+      mainRepoRoot,
       currentBranch,
       isDirty,
       baseRef: configured.baseRef,