Refresh workspace discovery between core API operations

[LadyBluenotes]

Problem

Process-global workspace caches retain roots, patterns, package directories, and workspace information without invalidation. Repeated public core API calls can miss workspace changes.

Evidence

Create a packages/* workspace with one member whose node_modules contains a skill dependency. Call listIntentSkills, add a second member with another skill dependency, and call listIntentSkills again in the same process: only the first skill appears. A fresh CLI process finds both.

Source: workspace caches.

Verified against main at 206e987 (@tanstack/intent 0.3.8), Node v24.12.0 on macOS arm64. Tests used installed dependencies and synthetic local fixtures.

Acceptance criteria

• Repeated core operations observe added and removed workspace members and changed workspace patterns.
• Any caching has an explicit operation/snapshot lifetime or tested refresh contract.
• Direct loading and npm/workspace source-kind decisions remain consistent after workspace changes.
• Regression tests compare repeated calls with a fresh discovery result.
• Existing direct-load and list benchmarks are checked for material regression.

Scope and priority

Priority: Medium. Type: bug.

Follow-up bug fix; not a v0.4.0 blocker. This reproduction does not demonstrate a memory leak. Preserve useful per-operation filesystem caches; do not introduce a watcher or daemon.