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

**New skill:**
- check-inline-code: Review inline code formatting (from feature branch)

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 <[email protected]>

Author: pinin4fjords

.claude/skills/check-inline-code/SKILL.md

@@ -0,0 +1,91 @@
+---
+name: Check Inline Code Formatting
+description: Review inline code in markdown files for proper formatting and syntax highlighting. Check for missing backticks on CLI flags, filenames, and code elements. Verify that inline syntax highlighting (#!groovy) is used appropriately. Use when reviewing documentation or quiz questions.
+---
+
+# Check Inline Code Formatting
+
+Review inline code in markdown files for proper formatting and appropriate use of syntax highlighting.
+
+## What to Check
+
+### 1. Missing Backticks
+
+The following should always be wrapped in backticks:
+
+**CLI flags and options:**
+
+- `-resume`, `-profile`, `-params-file`, `--input`, etc.
+
+**Filenames and paths:**
+
+- `nextflow.config`, `.command.sh`, `work/`, `modules/`, etc.
+
+**Commands:**
+
+- `nextflow run`, `nextflow log`, `docker run`, etc.
+
+**Code elements:**
+
+- Variable names: `params.input`, `outputDir`
+- Process names: `SAYHELLO`
+- Operators and methods: `collect()`, `map()`, `view()`
+- Directives: `container`, `publishDir`, `memory`
+
+### 2. Inline Syntax Highlighting
+
+Use `` `#!groovy code` `` for Groovy/Nextflow code that benefits from syntax colouring.
+
+**DO use `#!groovy` for:**
+
+- Variable interpolation: `` `#!groovy ${variable}` ``
+- Closures: `` `#!groovy { meta.id }` `` or `` `#!groovy .map { it * 2 }` ``
+- Method chains with closures: `` `#!groovy channel.of(1,2,3).map { it * 2 }` ``
+- String interpolation: `` `#!groovy "${greeting}-output.txt"` ``
+- Type declarations: `` `#!groovy param: String = 'value'` ``
+
+**DO NOT use `#!groovy` for:**
+
+- Single words or identifiers: use `` `outputDir` `` not `` `#!groovy outputDir` ``
+- Simple directives: use `` `container 'uri'` `` not `` `#!groovy container 'uri'` ``
+- Plain dot notation: use `` `processName.out` `` not `` `#!groovy processName.out` ``
+- Keywords alone: use `` `include` `` not `` `#!groovy include` ``
+
+**The rule:** Only use `#!groovy` when there's meaningful syntax structure (braces, interpolation, operators) that highlighting will visually enhance. A single word or simple expression gains nothing from syntax highlighting.
+
+### 3. Consistency
+
+- Similar code references should be formatted the same way throughout a document
+- Quiz answer options should have consistent formatting
+
+## Examples
+
+### Good inline code formatting
+
+```markdown
+Run the workflow with `nextflow run main.nf -resume`.
+
+The `#!groovy ${greeting}` variable is interpolated into the string.
+
+Set memory with `#!groovy process { withName: 'FOO' { memory = '4.GB' } }`.
+
+The `container` directive specifies the Docker image.
+
+Access outputs with `processName.out.outputName`.
+```
+
+### Bad inline code formatting
+
+```markdown
+<!-- Missing backticks -->
+
+Run the workflow with nextflow run main.nf -resume.
+
+<!-- Unnecessary #!groovy on single word -->
+
+The `#!groovy container` directive specifies the image.
+
+<!-- Missing #!groovy on closure -->
+
+Transform with `.map { it.toUpperCase() }`.
+```

.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