fix: repair broken skill references, fence nesting, and invisible unicode (#2568)

While implementing the Agent Plugin v1 spec in https://github.com/stbenjam/skillsaw/pull/483, I used this repository as a canonical real-world source for tests. Along the way its checks surfaced genuine correctness issues worth fixing regardless of tooling:

- Internal links that do not resolve (22): wrong relative paths, links whose targets are runtime output paths rather than bundled files (now inline code), a schemeless external URL parsed as a relative path, and links to files that do not exist (removed).

- Bundled skill files never referenced from their SKILL.md (14): each is now cited from the section where it is used, so nothing ships unreachable from the skill's instructions.

- Unclosed or mis-nested code fences (11): markdown templates embedding code blocks now use four-backtick outer fences so inner fences nest instead of closing the template early and leaking example content as live markdown; also removed stray orphan fences and closed an unterminated block at end of file.

- Invisible unicode (1): removed a zero-width space from a code example, a copy-paste artifact invisible to reviewers.

skills/threat-model-analyst/references/output-formats.md

@@ -567,7 +567,7 @@ Include at end of Executive Summary:
 
 ⚠️ **This ENTIRE section is REQUIRED.** Previous iterations skipped it entirely. Include ALL sub-sections below, even if tables are empty.
 
-```markdown
+````markdown
 ## Analysis Context & Assumptions
 
 ### Analysis Scope
@@ -601,7 +601,7 @@ Include at end of Executive Summary:
 <!-- Any other context from the user's prompt -->
 
 [Freeform notes provided by user]
-```
+````
 
 ### References Consulted Template