Codex Desktop WSL mode reuses Windows CODEX_HOME and fails SQLite migration checksum

[cidico]

What version of the Codex App are you using (From “About Codex” dialog)?

Codex App package: OpenAI.Codex_26.519.2736.0_x64__2p2nqsd0c76g0

Codex CLI versions observed:

• Windows app-server binary: codex-cli 0.133.0-alpha.1
• WSL app-server binary installed by the Desktop app: codex-cli 0.133.0-alpha.1
• Separately installed WSL CLI: codex-cli 0.133.0

Feedback ID: no-active-thread-019e4bf4-3082-7dd0-b08b-05abc340d31e

What subscription do you have?

Unknown / not sure from local diagnostics.

What platform is your computer?

Microsoft Windows NT 10.0.26200.0 x64

WSL distro:

Ubuntu Running WSL 2

What issue are you seeing?

The Codex Desktop app on Windows fails when WSL mode is enabled. The app starts a WSL app-server binary from the Windows CODEX_HOME, then the WSL binary fails to initialize SQLite state under /mnt/c/Users/<user>/.codex with a SQLx migration checksum mismatch.

The key error from the Codex Desktop log is:

[AppServerConnection] app_server_connection.closed code=1 ...
reason="Error: failed to initialize sqlite state runtime under /mnt/c/Users/<user>/.codex: failed to initialize state runtime at /mnt/c/Users/<user>/.codex: migration 1 was previously applied but has been modified"

The same failure is reproducible by running the WSL binary that the Desktop app installed:

CODEX_HOME=/mnt/c/Users/<user>/.codex \
  /mnt/c/Users/<user>/.codex/bin/wsl/ab950535f78f78c1/codex app-server --listen ws://127.0.0.1:0

Output:

codex-cli 0.133.0-alpha.1
Error: failed to initialize sqlite state runtime under /mnt/c/Users/<user>/.codex: failed to initialize state runtime at /mnt/c/Users/<user>/.codex: migration 1 was previously applied but has been modified

However, the Windows app-server binary of the same app version can initialize successfully against the Windows CODEX_HOME:

$env:CODEX_HOME="C:\Users\<user>\.codex"
C:\Users\<user>\AppData\Local\OpenAI\Codex\bin\3f4fb8cdd344abc7\codex.exe app-server --listen ws://127.0.0.1:0

Output:

codex-cli 0.133.0-alpha.1
codex app-server (WebSockets)
  listening on: ws://127.0.0.1:<port>

I also observed that manually setting the Desktop config back to Windows mode is not persistent. After launching the Desktop app, it rewrites C:\Users\<user>\.codex\config.toml back to WSL mode:

[desktop]
runCodexInWindowsSubsystemForLinux = true
integratedTerminalShell = "wsl"

When this happens, Desktop spawns:

spawnCommand=wsl.exe
executablePath=C:\Users\<user>\.codex\bin\wsl\ab950535f78f78c1\codex

Then initialization fails with the migration mismatch above.

What steps can reproduce the bug?

1. On Windows, install/open Codex Desktop.
2. Log in successfully.
3. Enable or switch the Desktop app to use WSL.
4. The app writes/uses CODEX_HOME=C:\Users\<user>\.codex, while the WSL runtime accesses it as /mnt/c/Users/<user>/.codex.
5. The Desktop app starts the WSL app-server via wsl.exe using the binary under C:\Users\<user>\.codex\bin\wsl\...\codex.
6. The WSL app-server exits with:

failed to initialize sqlite state runtime under /mnt/c/Users/<user>/.codex: failed to initialize state runtime at /mnt/c/Users/<user>/.codex: migration 1 was previously applied but has been modified

Additional reproduction details from local investigation:

• Resetting/emptying C:\Users\<user>\.codex and logging in again does not permanently fix the problem once WSL mode is selected.
• The Windows runtime can initialize the same state successfully.
• The WSL runtime cannot initialize the Windows .codex SQLite state through /mnt/c.
• I have a separate WSL CLI installed which uses /home/<user>/.codex; that state has a different migration count/checksum set and is not the same as the Desktop Windows CODEX_HOME.

What is the expected behavior?

Enabling WSL mode in Codex Desktop should not make the app unusable due to SQLite migration checksum mismatches.

Expected behavior could be one of:

• Desktop WSL mode should use a native Linux CODEX_HOME inside the distro, for example /home/<user>/.codex-desktop, instead of reusing C:\Users\<user>\.codex through /mnt/c.
• Or Windows and WSL runtimes should use byte-identical SQLx migration definitions/checksums and be able to share state safely.
• Or the app should detect incompatible Windows-vs-WSL SQLite state and recover or migrate automatically instead of failing startup.
• Or the UI should not silently rewrite runCodexInWindowsSubsystemForLinux = false back to true after the user/admin manually disables it to recover.

Additional information

Relevant Desktop log path:

C:\Users\<user>\AppData\Local\Packages\OpenAI.Codex_2p2nqsd0c76g0\LocalCache\Local\Codex\Logs\2026\05\21\codex-desktop-fa7f744d-09b5-4ecd-b0b3-53e4aa671603-33972-t0-i1-190442-0.log

Relevant log excerpts:

[wsl] eligible distro list listResult="NAME              STATE           VERSION\n* Ubuntu            Running         2\n  docker-desktop    Stopped         2"

[StdioConnection] stdio_transport_spawned argsCount=2 executablePath=C:\Users\<user>\.codex\bin\wsl\ab950535f78f78c1\codex pid=47224 spawnCommand=wsl.exe

[AppServerConnection] app_server_connection.closed code=1 connectionId=1 hasReason=true reason="Error: failed to initialize sqlite state runtime under /mnt/c/Users/<user>/.codex: failed to initialize state runtime at /mnt/c/Users/<user>/.codex: migration 1 was previously applied but has been modified" signal=null transport=stdio

[AppServerConnection] Codex CLI process exited classifiedAsExpected=false code=1 connectionId=1 signal=null transport=stdio

Related issues found before filing:

• WSL CLI cannot share Windows Codex App CODEX_HOME: migration 1 was previously applied but has been modified #23251
• WSL agent environment corrupts local state_5.sqlite migration on Windows #23841
• Codex App for Windows: WSL2 agent mode blocks launch due to SQLite migration mismatch #23893
• Windows Desktop WSL app-server fails to launch due to CRLF/LF SQLx migration checksum mismatch #23777

This issue includes the Feedback ID above and the observation that the Windows runtime succeeds while the WSL runtime fails against the same Desktop CODEX_HOME.

[github-actions]

Potential duplicates detected. Please review them and close your issue if it is a duplicate.

• Codex App for Windows: WSL2 agent mode blocks launch due to SQLite migration mismatch #23893
• Windows Desktop WSL app-server fails to launch due to CRLF/LF SQLx migration checksum mismatch #23777
• WSL agent environment corrupts local state_5.sqlite migration on Windows #23841
• Fixed: share how to fix, Codex GUI failed to launch because it could not initialize its local SQLite state DB. #23848
• Codex Desktop fails to start with migration 1 was previously applied but has been modified #23824

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[xdifu]

This is the same root-cause family as #23777 / #23787: the WSL/Linux Codex backend rejects a Windows-created SQLite DB because SQLx migration checksums differ at the CRLF-vs-LF byte level. Moving state_5.sqlite* / logs_2.sqlite* aside is a launch workaround, but it forces Codex to rebuild metadata instead of repairing the existing DBs.

For users who want to preserve local history metadata, I published a non-destructive repair tool: https://github.com/xdifu/codex-repair

Windows PowerShell / Windows Terminal:

git clone https://github.com/xdifu/codex-repair.git
cd codex-repair
python codex-repair.py fix --apply

If you run it from WSL bash to repair Windows Codex Desktop data, pass --codex-home "/mnt/c/Users/<WindowsUser>/.codex" so it does not target WSL's own ~/.codex.

It backs up the SQLite DBs, extracts the active backend's expected checksums, schema-verifies before rewriting _sqlx_migrations, and leaves ~/.codex/sessions/*.jsonl read-only.