diff --git a/src/targets/codex.ts b/src/targets/codex.ts
index dac7ed8a..0ed18d3a 100644
--- a/src/targets/codex.ts
+++ b/src/targets/codex.ts
@@ -91,10 +91,19 @@ export async function writeCodexBundle(outputRoot: string, bundle: CodexBundle):
   await cleanupRemovedAgents(agentsRoot, manifest, currentAgents)
   if (agents.length > 0) {
     for (const agent of agents) {
-      const agentFile = `${sanitizePathName(agent.name)}.toml`
+      const agentBaseName = sanitizePathName(agent.name)
+      const agentFile = `${agentBaseName}.toml`
+      // If the agent declares no sidecars, remove any same-basename sibling
+      // directory left behind by a prior install that did. The manifest-driven
+      // cleanupRemovedAgents sweep above only removes the sibling dir when the
+      // TOML itself is being removed; a same-name agent that loses its sidecar
+      // would otherwise leave an orphan directory.
+      if ((agent.sidecarDirs ?? []).length === 0 && isSafeManagedPath(agentsRoot, agentBaseName)) {
+        await fs.rm(path.join(agentsRoot, agentBaseName), { recursive: true, force: true })
+      }
       await writeText(path.join(agentsRoot, agentFile), renderCodexAgentToml(agent) + "\n")
       for (const sidecar of agent.sidecarDirs ?? []) {
-        await copyDir(sidecar.sourceDir, path.join(agentsRoot, sanitizePathName(agent.name), sidecar.targetName))
+        await copyDir(sidecar.sourceDir, path.join(agentsRoot, agentBaseName, sidecar.targetName))
       }
     }
   }
diff --git a/tests/codex-writer.test.ts b/tests/codex-writer.test.ts
index 9cd585c8..e46481f0 100644
--- a/tests/codex-writer.test.ts
+++ b/tests/codex-writer.test.ts
@@ -765,6 +765,87 @@ Workflow handoff:
     expect(installedSkill).not.toContain("/prompts:settings")
     expect(installedSkill).not.toContain("https://prompts:www.proofeditor.ai")
   })
+
+  test("removes orphan sidecar dir when retained agent declares no sidecars", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "codex-test-"))
+    const agentsRoot = path.join(tempRoot, ".codex", "agents")
+    const orphanDir = path.join(agentsRoot, "ce-foo", "stale-content")
+    await fs.mkdir(orphanDir, { recursive: true })
+    await fs.writeFile(path.join(orphanDir, "leftover.txt"), "stale", "utf8")
+    await fs.writeFile(path.join(agentsRoot, "ce-foo.toml"), "old-toml", "utf8")
+
+    const bundle: CodexBundle = {
+      prompts: [],
+      skillDirs: [],
+      generatedSkills: [],
+      agents: [
+        {
+          name: "ce-foo",
+          description: "Foo agent",
+          instructions: "Do foo.",
+        },
+      ],
+      mcpServers: {},
+    }
+
+    await writeCodexBundle(tempRoot, bundle)
+
+    expect(await entryExists(path.join(agentsRoot, "ce-foo"))).toBe(false)
+    expect(await exists(path.join(agentsRoot, "ce-foo.toml"))).toBe(true)
+  })
+
+  test("keeps sidecar dir when retained agent declares sidecars", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "codex-test-"))
+    const sidecarSource = await fs.mkdtemp(path.join(os.tmpdir(), "codex-sidecar-src-"))
+    await fs.writeFile(path.join(sidecarSource, "script.sh"), "#!/bin/sh\necho hi\n", "utf8")
+
+    const bundle: CodexBundle = {
+      prompts: [],
+      skillDirs: [],
+      generatedSkills: [],
+      agents: [
+        {
+          name: "ce-foo",
+          description: "Foo agent",
+          instructions: "Do foo.",
+          sidecarDirs: [{ sourceDir: sidecarSource, targetName: "scripts" }],
+        },
+      ],
+      mcpServers: {},
+    }
+
+    await writeCodexBundle(tempRoot, bundle)
+
+    const agentsRoot = path.join(tempRoot, ".codex", "agents")
+    expect(await exists(path.join(agentsRoot, "ce-foo.toml"))).toBe(true)
+    expect(await exists(path.join(agentsRoot, "ce-foo", "scripts", "script.sh"))).toBe(true)
+  })
+
+  test("leaves unrelated directories under agentsRoot alone", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "codex-test-"))
+    const agentsRoot = path.join(tempRoot, ".codex", "agents")
+    const unrelatedDir = path.join(agentsRoot, "ce-bar-extra")
+    await fs.mkdir(unrelatedDir, { recursive: true })
+    await fs.writeFile(path.join(unrelatedDir, "keep-me.txt"), "keep", "utf8")
+
+    const bundle: CodexBundle = {
+      prompts: [],
+      skillDirs: [],
+      generatedSkills: [],
+      agents: [
+        {
+          name: "ce-foo",
+          description: "Foo agent",
+          instructions: "Do foo.",
+        },
+      ],
+      mcpServers: {},
+    }
+
+    await writeCodexBundle(tempRoot, bundle)
+
+    expect(await exists(path.join(unrelatedDir, "keep-me.txt"))).toBe(true)
+  })
 })
 
 describe("renderCodexConfig", () => {