Anchor plugin paths at PLUGIN_ROOT and restore the layer-filter caveat

The adapter delegated index preparation to Entry's Preparation step, but that
step is written for the clone model: it runs `pwsh ./tools/Build-KnowledgeIndex.ps1`
from the checkout root. A plugin host's working directory is the user's own
project, so the path does not resolve and the index is never built. Because
knowledge-index.json is gitignored, a fresh install has none, and READ silently
degrades to path-based discovery. The adapter now resolves Entry's repo-relative
paths against PLUGIN_ROOT and names the absolute index build; the generator
resolves its own root, so it indexes and writes the right tree from any cwd.

Entry also asserted that pruning has always happened before it runs, which is
false for an installation that ships the whole tree. Entry now scopes that
guarantee to consumers that actually prune, and the caveat dropped in the
rewrite - that enabled-layers narrows discovery rather than denying access - is
restored in the adapter and summarized in the README.

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: 0b67b90d-e4b4-4b92-9684-726c72c43b3f

README.md

@@ -95,6 +95,11 @@ Entry remains the single owner of routing and index preparation;
 separation keeps standalone installation available without duplicating those
 policies in the plugin adapter.
 
+Note that a plugin install ships the entire tree, so `BCQUALITY_ENABLED_LAYERS`
+narrows discovery without removing any files. Layer selection is a filter here,
+not a deny mechanism — see [the adapter](skills/al-code-review/SKILL.md) for the
+difference from the pruned-clone model.
+
 The host adapter and internal action skill intentionally share the
 `al-code-review` name: they expose the same operation in two different skill
 formats. Their paths make the boundary explicit. The adapter lives under