Preserve existing Codex agent TOMLs on reinstall by tully-8888 · Pull Request #4711 · code-yeongyu/oh-my-openagent

tully-8888 · 2026-06-03T09:33:00Z

Summary

Preserve existing CODEX_HOME/agents/*.toml files instead of replacing them during Codex/LazyCodex reinstalls.
Materialize existing Unix symlinked agent TOMLs into regular user-owned files before refreshing the stable marketplace snapshot, so local edits survive snapshot rewrites.
Keep preserved user files out of .installed-agents.json so cleanup does not delete them, while still registering their [agents.*] config entries.
Mirror the behavior in the packaged packages/omo-codex/scripts installer path and update ultrawork docs.

Verification

bun run typecheck
bun test src/cli/install-codex/link-cached-plugin-agents.test.ts src/cli/install-codex/preserve-existing-codex-agents.test.ts
node --test packages/omo-codex/scripts/install-agent-links.test.mjs

Notes

bun run test:codex currently stops before reaching the Codex tests because build:lsp-tools-mcp runs npm --prefix packages/lsp-tools-mcp ci, but that package has no package-lock.json in this checkout.

Summary by cubic

Preserves existing agent TOMLs in CODEX_HOME/agents during Codex/LazyCodex reinstalls and marketplace updates so local edits aren’t overwritten. Converts old Unix symlinked agents to user-owned files and only installs missing agents.

Bug Fixes
- Materialize existing symlinked *.toml into regular files before refreshing the marketplace snapshot.
- Install agents only if missing: symlink on Unix, copy on Windows; never overwrite existing user files.
- Record only managed agent files in .installed-agents.json so preserved user files aren’t deleted on cleanup.
- Applied in both the CLI installer and packages/omo-codex/scripts; updated ultrawork docs and added tests.

^{Written for commit 1f981f7. Summary will update on new commits.}

github-actions · 2026-06-03T09:33:15Z

All contributors have signed the CLA. Thank you! ✅
_{Posted by the CLA Assistant Lite bot.}

chatgpt-codex-connector

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 1f981f7b8d

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

Open a pull request for review
Mark a draft as ready
Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

chatgpt-codex-connector · 2026-06-03T09:35:32Z

+  const materialized: string[] = []
+  const entries = await readdir(agentsDir, { withFileTypes: true })
+  for (const entry of entries) {
+    if (!entry.name.endsWith(".toml")) continue


Limit preservation to OMO-managed agent TOMLs

When a user already has their own CODEX_HOME/agents/custom.toml symlink, this loop treats it the same as an OMO-installed agent and the later rm/writeFile replaces the symlink with a regular copy, breaking dotfiles-managed or otherwise user-managed Codex agents. Both installer paths call this preservation step before linking OMO agents, so it should filter to the bundled/managed agent names or verify the symlink target is an OMO marketplace snapshot before materializing it.

Useful? React with 👍 / 👎.

cubic-dev-ai

5 issues found across 10 files

Confidence score: 2/5

There is a concrete data-loss risk in src/cli/install-codex/preserve-existing-codex-agents.ts and packages/omo-codex/scripts/install/preserve-existing-agents.mjs: the existing symlink is removed before the replacement file is safely written, so write failures can erase preserved agent TOML.
exists() in src/cli/install-codex/preserve-existing-codex-agents.ts swallows all lstat errors, which can hide real filesystem problems and silently skip preservation behavior when users most need it.
materializeExistingCodexAgentFiles is currently unguarded in src/cli/install-codex/install-codex.ts, so normal FS exceptions (permissions/races) can crash install; combined with the LinkedAgent.target semantic mismatch in src/cli/install-codex/link-cached-plugin-agents.ts, this creates meaningful regression risk.
Pay close attention to src/cli/install-codex/preserve-existing-codex-agents.ts, packages/omo-codex/scripts/install/preserve-existing-agents.mjs, src/cli/install-codex/install-codex.ts, src/cli/install-codex/link-cached-plugin-agents.ts - preservation flow can lose user config, mask FS failures, or fail during install.

Prompt for AI agents (unresolved issues)


Check if these issues are valid — if so, understand the root cause of each and fix them. If appropriate, use sub-agents to investigate and fix each issue separately.


<file name="src/cli/install-codex/preserve-existing-codex-agents.ts">

<violation number="1" location="src/cli/install-codex/preserve-existing-codex-agents.ts:17">
P1: Symlink is removed before replacement file is safely written, risking loss of agent config on write failure</violation>

<violation number="2" location="src/cli/install-codex/preserve-existing-codex-agents.ts:35">
P2: `exists()` helper swallows all lstat errors, masking real filesystem failures and silently skipping preservation logic.</violation>
</file>

<file name="src/cli/install-codex/link-cached-plugin-agents.ts">

<violation number="1" location="src/cli/install-codex/link-cached-plugin-agents.ts:34">
P2: `LinkedAgent.target` has mixed semantics depending on `managed` flag: it is the bundled source path when `managed=true`, but the destination (`linkPath`) when `managed=false`. This silently breaks the contract that `target` represents the source artifact.</violation>
</file>

<file name="src/cli/install-codex/install-codex.ts">

<violation number="1" location="src/cli/install-codex/install-codex.ts:83">
P2: `materializeExistingCodexAgentFiles` call is unguarded: permission errors, race-condition ENOENT on `readdir`/`lstat`, and other FS exceptions can crash the entire install. Wrap it in a try-catch so agent-preservation failures don't hard-block the installer.</violation>
</file>

<file name="packages/omo-codex/scripts/install/preserve-existing-agents.mjs">

<violation number="1" location="packages/omo-codex/scripts/install/preserve-existing-agents.mjs:19">
P2: Don't remove the old agent symlink before the replacement file is safely written; a write failure here can erase the user's preserved TOML.</violation>
</file>

_{Reply with feedback, questions, or to request a fix.

Re-trigger cubic}

cubic-dev-ai · 2026-06-03T09:49:20Z

+    if (!stat.isSymbolicLink()) continue
+
+    const content = await readExistingSymlinkContent(agentPath)
+    await rm(agentPath, { force: true })


P1: Symlink is removed before replacement file is safely written, risking loss of agent config on write failure

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At src/cli/install-codex/preserve-existing-codex-agents.ts, line 17: <comment>Symlink is removed before replacement file is safely written, risking loss of agent config on write failure</comment> <file context> @@ -0,0 +1,42 @@ + if (!stat.isSymbolicLink()) continue + + const content = await readExistingSymlinkContent(agentPath) + await rm(agentPath, { force: true }) + if (content === null) continue + </file context>

cubic-dev-ai · 2026-06-03T09:49:20Z

+  }
+}
+
+async function exists(path: string): Promise<boolean> {


P2: exists() helper swallows all lstat errors, masking real filesystem failures and silently skipping preservation logic.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At src/cli/install-codex/preserve-existing-codex-agents.ts, line 35: <comment>`exists()` helper swallows all lstat errors, masking real filesystem failures and silently skipping preservation logic.</comment> <file context> @@ -0,0 +1,42 @@ + } +} + +async function exists(path: string): Promise<boolean> { + try { + await lstat(path) </file context>

cubic-dev-ai · 2026-06-03T09:49:20Z

+    const installed = platform === "win32"
+      ? await copyIfMissing(linkPath, agentPath)
+      : await symlinkIfMissing(linkPath, agentPath)
+    linked.push({ name: basename(agentPath), path: linkPath, target: installed.target, managed: installed.managed })


P2: LinkedAgent.target has mixed semantics depending on managed flag: it is the bundled source path when managed=true, but the destination (linkPath) when managed=false. This silently breaks the contract that target represents the source artifact.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At src/cli/install-codex/link-cached-plugin-agents.ts, line 34: <comment>`LinkedAgent.target` has mixed semantics depending on `managed` flag: it is the bundled source path when `managed=true`, but the destination (`linkPath`) when `managed=false`. This silently breaks the contract that `target` represents the source artifact.</comment> <file context> @@ -27,16 +28,14 @@ export async function linkCachedPluginAgents(input: { + const installed = platform === "win32" + ? await copyIfMissing(linkPath, agentPath) + : await symlinkIfMissing(linkPath, agentPath) + linked.push({ name: basename(agentPath), path: linkPath, target: installed.target, managed: installed.managed }) } await writeManifest( </file context>

cubic-dev-ai · 2026-06-03T09:49:20Z

    installed.push(plugin)
  }

+  await materializeExistingCodexAgentFiles(codexHome)


P2: materializeExistingCodexAgentFiles call is unguarded: permission errors, race-condition ENOENT on readdir/lstat, and other FS exceptions can crash the entire install. Wrap it in a try-catch so agent-preservation failures don't hard-block the installer.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At src/cli/install-codex/install-codex.ts, line 83: <comment>`materializeExistingCodexAgentFiles` call is unguarded: permission errors, race-condition ENOENT on `readdir`/`lstat`, and other FS exceptions can crash the entire install. Wrap it in a try-catch so agent-preservation failures don't hard-block the installer.</comment> <file context> @@ -79,6 +80,7 @@ export async function runCodexInstaller(options: CodexInstallOptions = {}): Prom installed.push(plugin) } + await materializeExistingCodexAgentFiles(codexHome) const agentSourceRoots = await agentSourceRootsForInstall({ codexHome, </file context>

Suggested change

await materializeExistingCodexAgentFiles(codexHome)

try {

await materializeExistingCodexAgentFiles(codexHome)

} catch (error) {

log(`Warning: could not materialize existing agent files: ${error instanceof Error ? error.message : String(error)}`)

}

cubic-dev-ai · 2026-06-03T09:49:20Z

+		if (!stat.isSymbolicLink()) continue;
+
+		const content = await readExistingSymlinkContent(agentPath);
+		await rm(agentPath, { force: true });


P2: Don't remove the old agent symlink before the replacement file is safely written; a write failure here can erase the user's preserved TOML.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At packages/omo-codex/scripts/install/preserve-existing-agents.mjs, line 19: <comment>Don't remove the old agent symlink before the replacement file is safely written; a write failure here can erase the user's preserved TOML.</comment> <file context> @@ -0,0 +1,35 @@ + if (!stat.isSymbolicLink()) continue; + + const content = await readExistingSymlinkContent(agentPath); + await rm(agentPath, { force: true }); + if (content === null) continue; + </file context>

tully-8888 · 2026-06-03T10:01:38Z

I have read the CLA Document and I hereby sign the CLA

fix: preserve existing Codex agent TOMLs

1f981f7

tully-8888 mentioned this pull request Jun 3, 2026

Preserve customized Codex agent reasoning effort across LazyCodex reinstall code-yeongyu/lazycodex#18

Closed

chatgpt-codex-connector Bot reviewed Jun 3, 2026

View reviewed changes

cubic-dev-ai Bot reviewed Jun 3, 2026

View reviewed changes

github-actions Bot added a commit that referenced this pull request Jun 3, 2026

@tully-8888 has signed the CLA in #4711

63a856f

snowykr mentioned this pull request Jun 6, 2026

[LazyCodex Bug]: service_tier customizations are overwritten on reinstall or auto-update #5020

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Preserve existing Codex agent TOMLs on reinstall#4711

Preserve existing Codex agent TOMLs on reinstall#4711
tully-8888 wants to merge 1 commit into
code-yeongyu:devfrom
tully-8888:fix/preserve-existing-codex-agents

tully-8888 commented Jun 3, 2026 •

edited by cubic-dev-ai Bot

Loading

Uh oh!

github-actions Bot commented Jun 3, 2026 •

edited

Loading

Uh oh!

chatgpt-codex-connector Bot left a comment

Uh oh!

chatgpt-codex-connector Bot Jun 3, 2026

Uh oh!

cubic-dev-ai Bot left a comment

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Uh oh!

tully-8888 commented Jun 3, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

Conversation

tully-8888 commented Jun 3, 2026 • edited by cubic-dev-ai Bot Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Summary

Verification

Notes

Summary by cubic

Uh oh!

github-actions Bot commented Jun 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

chatgpt-codex-connector Bot left a comment

Choose a reason for hiding this comment

💡 Codex Review

Uh oh!

chatgpt-codex-connector Bot Jun 3, 2026

Choose a reason for hiding this comment

Uh oh!

cubic-dev-ai Bot left a comment

Choose a reason for hiding this comment

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Choose a reason for hiding this comment

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Choose a reason for hiding this comment

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Choose a reason for hiding this comment

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Choose a reason for hiding this comment

Uh oh!

cubic-dev-ai Bot Jun 3, 2026

Choose a reason for hiding this comment

Uh oh!

tully-8888 commented Jun 3, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

tully-8888 commented Jun 3, 2026 •

edited by cubic-dev-ai Bot

Loading

github-actions Bot commented Jun 3, 2026 •

edited

Loading