refactor: migrate commands to user-invocable skills

Claude Code has unified commands into skills with the user-invocable
frontmatter field. This migration:

- Converts 20 commands to skills with user-invocable: true
- Consolidates docs into single writing-capabilities.md
- Rewrites capability-writing skill for unified model
- Updates CLAUDE.md, Makefile, and other references
- Removes commands/ directory

Skills now have two types:
- user-invocable: true - workflows users trigger with /name
- user-invocable: false - background knowledge auto-loaded

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

learnings/README.md

@@ -4,7 +4,7 @@ This folder captures learnings from retrospectives and day-to-day work. Learning
 
 1. **Historical record**: What we learned and when
 2. **Governance reference**: Why we work the way we do
-3. **Encoding source**: Input that gets encoded into skills, commands, and agents
+3. **Encoding source**: Input that gets encoded into skills and agents
 
 ## The Learning Flow
 
@@ -17,7 +17,7 @@ Experience → Learning captured → Encoded into system → Knowledge is action
             - Periodic review
 ```
 
-Learnings are **not** the final destination. They are inputs that get encoded into commands, skills, and agents where Claude can actually use them. But we keep the learning file as a record of *why* we encoded what we did.
+Learnings are **not** the final destination. They are inputs that get encoded into skills and agents where Claude can actually use them. But we keep the learning file as a record of *why* we encoded what we did.
 
 ## Writing a Learning
 
@@ -40,8 +40,7 @@ The insight we gained. Be specific and actionable.
 Where this learning has been (or will be) encoded:
 
 - `skills/xxx/SKILL.md` - What was added/changed
-- `commands/xxx.md` - What was added/changed
-- `agents/xxx/agent.md` - What was added/changed
+- `agents/xxx/AGENT.md` - What was added/changed
 
 If not yet encoded, note: "Pending: Issue #XX"
 
@@ -54,7 +53,7 @@ What this learning means for how we work going forward. This is the "why" that j
 
 1. **Capture the learning** in this folder
 2. **Create an issue** to encode it into the appropriate location
-3. **Update the skill/command/agent** with the encoded knowledge
+3. **Update the skill/agent** with the encoded knowledge
 4. **Update the learning file** with the "Encoded In" references
 
 The goal: Claude should be able to *use* the learning, not just *read* about it.
@@ -63,8 +62,8 @@ The goal: Claude should be able to *use* the learning, not just *read* about it.
 
 | Learning Type | Encode In |
 |---------------|-----------|
-| How to use a tool | `skills/` |
-| Workflow improvement | `commands/` |
+| How to use a tool | `skills/` (background skill) |
+| Workflow improvement | `skills/` (user-invocable skill) |
 | Subtask behavior | `agents/` |
 | Organization belief | `manifesto.md` |
 | Product direction | `vision.md` (in product repo) |