[Bug]: Claude launch args --settings is silently replaced by T3's own SDK settings #15073

Filed by Claude (an AI agent) on behalf of @jlui17.

Before submitting

• I searched existing issues and did not find a duplicate.
• I included enough detail to reproduce or investigate the problem.

The closest reports are #13934 (--append-system-prompt-file ignored) and #7577 (launch args outranked by the permission mode). Both are the same kind of conflict between a launch arg and an SDK option T3 sets, but neither covers --settings.

Area

apps/server

Steps to reproduce

1. In Settings → Providers → Claude, set Launch args to --settings '{"skillOverrides":{"<any-skill-name>":"off"}}' (a path to a settings file behaves the same).
2. Start a new Claude thread.
3. Ask the agent whether <any-skill-name> is in its skill list.

Expected behavior

The session starts with the user's settings merged with T3's own settings, so the skill is hidden. If T3 can't support --settings in launch args, it should say so instead of dropping the flag.

Actual behavior

The user's --settings never reaches Claude Code, so the skill is still listed. Nothing warns that the flag was dropped.

The cause:

• ClaudeAdapterV2 passes the launch args through as extraArgs, so --settings lands in extraArgs.settings (ClaudeAdapterV2.ts:803–807).
• T3 also builds its own SDK settings (model options, auto-compaction, showThinkingSummaries: true) and sets options.settings on the normal path (818–834, 857–870).
• The Agent SDK (0.3.276) copies extraArgs and then replaces settings with options.settings (sdk.mjs): let Rn={...a??{}};if(this.options.settings)Rn.settings=this.options.settings;

So whenever T3 sets any setting of its own, a user's --settings is overwritten.

A possible fix: when extraArgs.settings is present, read it (inline JSON or a file path) and merge it under T3's settings before passing options.settings, then drop it from extraArgs.

Impact

Minor bug or occasional failure

Version or commit

0.0.46-nightly.20261003.2610 (8ed276c); the same code is on main @ fed41fa.

Environment

Linux (Arch/Omarchy), T3 Code server nightly, Claude Code 2.1.286, Claude Agent SDK 0.3.276, Claude provider.

Workaround

Point the Claude provider's binary path at a small wrapper script that merges the extra settings into the --settings JSON the SDK passes, then runs the real claude. A separate CLAUDE_CONFIG_DIR with its own settings.json also works, but it splits auth and history from the normal config.