refactor(bin): cut per-invocation load and repair broken skill references

diagnose read its feedback-loops reference unconditionally, so every
invocation paid for guidance most runs never used; the read is conditional
again and the per-invocation cost drops from 1,278 to 831 words. Its HITL
template moves to assets/ because it is copied out, not read as reference.
prototype's two branch flows move into references/ for the same reason —
only one branch is ever taken.

research could not search the codebase it was asked to research without Grep
and Glob. caveman's description had grown into a paragraph where one sentence
carries the trigger. Four references pointed at things that do not exist: a
to-prd skill, a /setup-matt-pocock-skills command, two cross-skill ../ links
that only resolve in the source tree, and two places calling this project's
Gitea host GitHub.

Addresses #114.

plugins/bin/.apm/skills/research/SKILL.md

@@ -8,10 +8,12 @@ description: >-
 metadata:
   category: research
 allowed-tools:
-  - WebSearch
-  - WebFetch
+  - Grep
+  - Glob
   - Read
   - Write
+  - WebSearch
+  - WebFetch
   - mcp__context7__resolve-library-id
   - mcp__context7__query-docs
 model: sonnet
@@ -61,4 +63,4 @@ Merge every set of notes, Context7 and web alike, by topic area. Read `reference
 
 Spell the `sources.md` field names exactly as `references/file-format.md` gives them. The downstream provenance validator matches them literally; prose in their place parses as nothing, and the check passes having verified nothing.
 
-If no topic area has content, write nothing at all, `sources.md` included, and report what was searched. A directory of empty files is worse than an honest miss.
+If no topic area has content, write nothing at all, `sources.md` included, and report what was searched.