test(repository-plugin): drop the skill contribution from the preset-composed e2e

The agent plane of this stack's compositions lives behind agent presets,
whose per-preset skills realm has no seam for a deployment-level provider
yet: the fixture's dsh.skills made the prepared wrapper wait forever on a
host skills registry the web/headless profiles no longer compose. Remove
the skill root and its assertions from the fixture and record the gap in
the package's Known Limitations; MCP and entry contributions stay covered
because the tools registry is host-plane and layered.

apps/cli/tests/fixtures/github-repository-plugin/skills/github-source-proof/SKILL.md

@@ -1,6 +0,0 @@
----
-name: github-source-proof
-description: Proves that dsh installed a private repository Plugin from an exact GitHub source.
----
-
-This skill exists only in the GitHub repository source fixture.