@jubi - right now the toggle Include third-party Plugins, Skills, and other configs is an IDE-only setting. In ~/.cursor/cli-config.json docs Configuration | Cursor Docs there is no equivalent flag documented, it only has editor and permissions. Also, the cursor-agent CLI handles skills differently in general. There are a few parity gap reports, for example this one Cursor-agent CLI does not register skills from plugins (IDE does — parity gap) and this one Cursor CLI does not load ./claude/skills, so skills behavior in CLI vs IDE is not symmetric right now. I marked it internally as a gap. When we fix hidden-dirs filtering, we’ll also take a look at the CLI side.
@Demianight - this looks similar by symptoms, but it’s a different case overall. Built-in skills from ~/.cursor/skills-cursor/ are currently seeded automatically and re-populated on update, and that’s by design at this stage. What you want is a first-class option to disable built-ins skills/subagents/commands. That’s a reasonable feature request, but it’s broader than the hidden directories bug from the original thread. Can you open a separate thread for it? That’ll make it easier to track and prioritize separately, without mixing it with the fix for scanning .claude/skills. The chflags uchg workaround is valid for now, even if it’s a bit fragile.
There’s already a similar feature request you can upvote in the meantime: Toggle (or allowlist) for Agent Skills roots Toggle (or allowlist) for Agent Skills roots — stop loading ~/.claude/skills and ~/.codex/skills when I only want .cursor / .agents. It’s mostly about external roots, but it’s the same general direction.