Refactor Claude skills for better delegation and reduced verbosity

This refactor addresses issues where skills that should invoke other
skills often skip those invocations. Key changes:

**Stronger delegation patterns:**
- Add "Skill Dependencies (MANDATORY)" tables at top of skills
- Use explicit ">>> STOP. INVOKE /skill NOW." checkpoint blocks
- Replace passive "Use Skill tool with..." language with imperative commands

**Reduced verbosity:**
- run-tutorial: 408 → 214 lines (-48%)
- validate: 249 → 194 lines (-22%)
- Extract detailed content to reference files

**New reference files:**
- run-tutorial/references/acceptable-differences.md: What to flag vs ignore
- run-tutorial/references/pr-workflow.md: PR creation workflow
- shared/repo-conventions.md: Directory mapping used by multiple skills

All critical assertions and checks are preserved, either inline or in
reference files. Writing style checks from PR #774 are maintained.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: pinin4fjords

.claude/skills/find-todos/SKILL.md

@@ -7,15 +7,7 @@ description: Search markdown files, Nextflow scripts, and config files for TODO/
 
 Search the training materials codebase for TODO and FIXME comments to identify pending work.
 
-## Working Directory
-
-**IMPORTANT**: All commands in this skill must be executed from the repository root directory.
-
-- The repository root is the directory containing `mkdocs.yml`, `docs/`, and `.github/`
-- Verify you are in the correct directory before running any commands (check for these files/folders)
-- All file paths in this skill are relative to the repository root
-- Do not change directories during skill execution
-- Use paths relative to repository root only
+Execute from repository root. See [../shared/repo-conventions.md](../shared/repo-conventions.md) for directory structure.
 
 ## Tasks to Perform