fix: remove the obsidian MCP server and the unreadable .mcp.json files

718c79a deleted every per-plugin .claude-plugin/plugin.json, which
reclassified each package from a marketplace plugin to a plain apm
package. That silently broke MCP propagation: apm_cli/deps/plugin_parser.py
maps a plugin-root .mcp.json into .apm/.mcp.json, and that code path runs
only for marketplace plugins. With no manifest, apm never reads the file.

Reproduced on ref-pinned consumer clones: at the parent commit a consumer
receives the obsidian server, at HEAD it receives none, and on upgrade apm
prints "Removed stale MCP server 'obsidian' from .mcp.json". This repo
consumes its own plugins through apm (ADR-0018), so the tracked root
.mcp.json would have been rewritten to an empty server map on the next
lock re-resolve -- silent tool loss plus unexplained working-tree drift.

The server is removed entirely rather than relocated to .apm/. It was
already a standing question (SIMPLIFICATION-AUDIT finding 37, deferred on
2026-09-13 pending confirmation, now confirmed), and plugins/bin/apm.yml
declares dependencies.mcp: [] -- apm's supported mechanism was never used.
All seven .mcp.json files go; the root one is apm-generated output and is
now gitignored alongside the other install artifacts.

ADR-0011's deferred ".mcp.json wiring gap" is moot twice over -- the
install route it blocked no longer exists and neither does the file --
and ADR-0018 records why it lost its only worked example of MCP
propagation. apm.lock.yaml still carries the server; it clears on the
first apm update after this reaches the default branch.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YR2CjVumUbEGWcMikcoXBD

docs/spec/architecture.md

@@ -48,7 +48,7 @@ One compiler produces the generated content in the tree:
 
 apm is the only supported install path. A flat `skills/`, `agents/`, `hooks/` mirror used to be compiled to each plugin root so Claude Code's installer could convention-scan it, alongside a per-plugin `.claude-plugin/plugin.json` and `.github/plugin/plugin.json`; both are gone, together with native `claude plugin install` support. apm reads `plugins/<name>/apm.yml` and deploys from `.apm/` directly, and never probed those manifests.
 
-`.apm/` is the sole hand-edited authoring source for plugin content. Hand-authored material that is not an `.apm/` primitive — `README.md`, `docs/`, `bin/`, `sources.md`, `.mcp.json`, and per-plugin extras such as `plugins/gitea/references/` and `plugins/bin/evals/` — lives at the plugin **root**. A hand-edit to the generated `.claude-plugin/marketplace.json` is reported as drift by the `apm-pack-check-clean` pre-push hook.
+`.apm/` is the sole hand-edited authoring source for plugin content. Hand-authored material that is not an `.apm/` primitive — `README.md`, `docs/`, `bin/`, `sources.md`, and per-plugin extras such as `plugins/gitea/references/` and `plugins/bin/evals/` — lives at the plugin **root**. A hand-edit to the generated `.claude-plugin/marketplace.json` is reported as drift by the `apm-pack-check-clean` pre-push hook.
 
 Plugin-root documentation belongs in `docs/`. That convention is older than the mirror's removal: a hand-written `README.md` placed inside a mirrored directory used to be destroyed by the next sync with no drift report, which cost the repo one document — `plugins/kyberforge/hooks/README.md`, since restored to `plugins/kyberforge/docs/hooks.md`.