fix(skill): plugin bundle payload files are registered as standalone skills in v2 discovery

What

FileSkillDiscovery registers every loose .md it finds at a top-level root besides SKILL.md. When the root dir IS a bundle (it has its own SKILL.md), the bundle's payload files get registered as standalone skills too — the same over-registration the legacy v1 scanner had (#2127, closed after the v1 package was removed in #3542).

Reproduction on current main

Root laid out like a mattpocock-style bundle:

teach/SKILL.md            (name: teach)
teach/GLOSSARY-FORMAT.md  (payload, not a skill)

new FileSkillDiscovery().discover([{ path: "…/teach", source: "extra", plugin: { id: "mattpocock-skills" } }]) returns:

discovered: [ 'GLOSSARY-FORMAT', 'teach' ]

Expected: [ 'teach' ] — payload files alongside a bundle's SKILL.md belong to the bundle, they are not standalone skills.

The relevant loop is in packages/agent-core-v2/src/features/skill/catalog/fileSkillDiscovery.ts at the isTopLevel branch: it registers the root SKILL.md and then still iterates the dir's remaining .md entries as flat skills. Loose top-level .md in a root WITHOUT a SKILL.md is an intentional shape (pinned by the existing "discovers a flat .md skill at the root top level" test), so the narrow fix is to skip that flat loop only when the root dir has its own SKILL.md.

I have the reproduction as a failing test and a patch ready; PR coming.

Read packages/agent-core-v2/src/features/skill/catalog/fileSkillDiscovery.ts, focusing on the isTopLevel branch and its flat-skill test. Run the failing reproduction, then verify that a bundle root returns only its SKILL.md while a root without SKILL.md still discovers loose .md skills. Note that a patch is already ready and a pull request is planned.