refactor(agents): scope customization to monorepo

Move Pi runtime resources into project-local .pi directories and keep shell modules responsible for installing Pi, Herdr, gitea-axi, and Pi package patches.

Remove legacy global agent context, Claude Code customization, the global skills bridge, and the external skills flake input.

src/skills/README.md

@@ -0,0 +1,28 @@
+# Skills
+
+This directory contains monorepo-owned agent skill sources.
+
+## Layout
+
+```text
+src/skills/                     Monorepo-owned skill sources
+.pi/skills/                     Monorepo-wide enabled Pi skill symlinks
+src/<project>/skills/           Project-owned skill sources
+src/<project>/.pi/skills/       Project-specific enabled Pi skill symlinks
+```
+
+## Source ownership
+
+Use `src/skills/` for skills that support workflows across the monorepo.
+Keep project-specific skills inside the project that owns them.
+
+For example, a `gitea-axi` skill belongs with the `gitea-axi` project source.
+A general commit or review workflow skill belongs in `src/skills/`.
+
+## Enablement
+
+Enable Pi skills with symlinks.
+Do not copy skill sources into `.pi/skills/`.
+
+Use root `.pi/skills/` for skills available anywhere inside the monorepo.
+Use `src/<project>/.pi/skills/` for skills available only in that project subtree.