refactor: move skills into subdirectory

Amolith created

Enables cleaner stow usage: `stow -d skills -t ~/.config/crush/skills .`

Assisted-by: Claude Opus 4.5 via Crush

Change summary

AGENTS.md                                                           |  8 
README.md                                                           | 44 
skills/authoring-skills/SKILL.md                                    |  0 
skills/authoring-skills/references/checklist.md                     |  0 
skills/authoring-skills/references/patterns.md                      |  0 
skills/authoring-skills/references/specification.md                 |  0 
skills/formatting-commits/SKILL.md                                  |  0 
skills/formatting-commits/references/installing-formatted-commit.md |  0 
skills/invoking-subagents/SKILL.md                                  |  0 
skills/invoking-subagents/references/installing-synu.md             |  0 
skills/querying-documentation/SKILL.md                              |  0 
skills/querying-documentation/references/installing-doc-agent.md    |  0 
skills/resolving-secrets/SKILL.md                                   |  0 
skills/resolving-secrets/references/installing-opx.md               |  0 
14 files changed, 27 insertions(+), 25 deletions(-)

Detailed changes

AGENTS.md πŸ”—

@@ -4,10 +4,10 @@ Amolith's collection of Agent Skillsβ€”markdown-based documentation that extends
 
 ## Repository Structure
 
-Each top-level directory is a skill. A skill's directory name **must match** its `name` frontmatter field.
+Each directory under `skills/` is a skill. A skill's directory name **must match** its `name` frontmatter field.
 
 ```
-skill-name/
+skills/skill-name/
 β”œβ”€β”€ SKILL.md          # Required: YAML frontmatter + markdown instructions
 β”œβ”€β”€ references/       # Optional: additional documentation loaded on-demand
 β”œβ”€β”€ scripts/          # Optional: executable code
@@ -16,10 +16,10 @@ skill-name/
 
 ## Creating/Editing Skills
 
-The `authoring-skills/` directory has the necessary info for, well, authoring skills.
+The `skills/authoring-skills/` directory has the necessary info for, well, authoring skills.
 
 ## Design Principles
 
 1. Progressive disclosure: Frontmatter loads at startup; SKILL.md body loads on activation; references/ load on-demand
 2. Conciseness over completeness: Every token competes for context window space
-3. Appropriate freedom: Match instruction specificity to task fragility (see `authoring-skills/references/patterns.md`)
+3. Appropriate freedom: Match instruction specificity to task fragility (see `skills/authoring-skills/references/patterns.md`)

README.md πŸ”—

@@ -13,26 +13,23 @@ agent capabilities through a standardised format.
 
 ## Available Skills
 
-- [authoring-skills](authoring-skills/SKILL.md): Creates well-structured
-  Agent Skills following best practices. Use when writing new skills,
-  reviewing existing skills, or when the user mentions skill authoring.
-
-- [formatting-commits](formatting-commits/SKILL.md): Creates commits
-  strictly following Conventional Commits format via the
+- [authoring-skills](skills/authoring-skills/SKILL.md): Creates
+  well-structured Agent Skills following best practices. Use when
+  writing new skills, reviewing existing skills, or when the user
+  mentions skill authoring.
+- [formatting-commits](skills/formatting-commits/SKILL.md): Creates
+  commits strictly following Conventional Commits format via the
   `formatted-commit` CLI.
-
-- [invoking-subagents](invoking-subagents/SKILL.md): Invokes ad-hoc
-  subagents to read through lots of data and extract relevant
+- [invoking-subagents](skills/invoking-subagents/SKILL.md): Invokes
+  ad-hoc subagents to read through lots of data and extract relevant
   information. Useful for exploring repositories, reading git logs,
   reviewing large diffs.
-
-- [querying-documentation](querying-documentation/SKILL.md): Spawns
-  focused agents to search specific language/framework documentation and
-  answer moderately complex queries.
-
-- [resolving-secrets](resolving-secrets/SKILL.md): Wraps shell commands
-  to resolve secret references in environment variables. Use when
-  invoking `synu`, `crush`, `gh`, `hut`, etc.
+- [querying-documentation](skills/querying-documentation/SKILL.md):
+  Spawns focused agents to search specific language/framework
+  documentation and answer moderately complex queries.
+- [resolving-secrets](skills/resolving-secrets/SKILL.md): Wraps shell
+  commands to resolve secret references in environment variables. Use
+  when invoking `synu`, `crush`, `gh`, `hut`, etc.
 
 ## Installation
 
@@ -50,19 +47,24 @@ Get it from your preferred/available package manager (definitely true on
 Linux, I assume so on macOS and Windows)
 
 ```sh
+# Install all skills
+stow -d skills -t ~/.config/crush/skills .
+
 # Install specific skills
-stow -t ~/.config/crush/skills authoring-skills formatting-commits
+stow -d skills -t ~/.config/crush/skills authoring-skills …
 
 # Remove a skill
-stow -D -t ~/.config/crush/skills formatting-commits
+stow -D -d skills -t ~/.config/crush/skills formatting-commits
 ```
 
 ### With symlinks
 
 ```sh
+# Install all skills
+for s in skills/*/; do ln -s "$PWD/$s" ~/.config/crush/skills/; done
+
 # Install specific skills
-ln -s "$PWD/authoring-skills" ~/.config/crush/skills/
-ln -s "$PWD/formatting-commits" ~/.config/crush/skills/
+ln -s "$PWD/skills/authoring-skills" ~/.config/crush/skills/
 
 # Remove a skill
 rm ~/.config/crush/skills/formatting-commits