Hey @azhang, quick update: the fix for excessive skill loading from hidden directories inside ~/.claude/skills/ and for duplicate skill loading landed in Cursor 3.17. Please update to 3.17 or newer and give it another try.
If anything from hidden folders still ends up in the initial context, or duplicates don’t collapse, for example your GStack ~/.agent/skills vs ~/.claude/skills case, drop a screenshot of the context and we’ll take another look.
Separately, the request to disable built-in skills from ~/.cursor/skills-cursor/ now lives in its own thread: First-class option to disable built-in skills from ~/.cursor/skills-cursor/
cc @jubi @zar42stra