fix: skill integration bugs, transitive dep cleanup, and skill_integrator simplification

docs/cli-reference.md

@@ -270,16 +270,20 @@ apm uninstall microsoft/apm-sample-package --dry-run
 |------|----------|
 | Package entry | `apm.yml` dependencies section |
 | Package folder | `apm_modules/owner/repo/` |
+| Transitive deps | `apm_modules/` (orphaned transitive dependencies) |
 | Integrated prompts | `.github/prompts/*-apm.prompt.md` |
 | Integrated agents | `.github/agents/*-apm.agent.md` |
 | Integrated chatmodes | `.github/agents/*-apm.chatmode.md` |
 | Claude commands | `.claude/commands/*-apm.md` |
 | Skill folders | `.github/skills/{folder-name}/` |
+| Lockfile entries | `apm.lock` (removed packages + orphaned transitives) |
 
 **Behavior:**
 - Removes package from `apm.yml` dependencies
 - Deletes package folder from `apm_modules/`
+- Removes orphaned transitive dependencies (npm-style pruning via `apm.lock`)
 - Removes all integrated files with `-apm` suffix that originated from the package
+- Updates `apm.lock` (or deletes it if no dependencies remain)
 - Cleans up empty parent directories
 - Safe operation: only removes APM-managed files (identified by `-apm` suffix)
 
@@ -336,7 +340,7 @@ apm deps COMMAND [OPTIONS]
 
 #### `apm deps list` - 📋 List installed APM dependencies
 
-Show all installed APM dependencies in a Rich table format with context files and agent workflows.
+Show all installed APM dependencies in a Rich table format with per-primitive counts.
 
 ```bash
 apm deps list
@@ -350,24 +354,22 @@ apm deps list
 
 **Sample Output:**
 ```
-┌─────────────────────┬─────────┬──────────────┬─────────────┬─────────────┐
-│ Package             │ Version │ Source       │ Context     │ Workflows   │
-├─────────────────────┼─────────┼──────────────┼─────────────┼─────────────┤
-│ compliance-rules    │ 1.0.0   │ main         │ 2 files     │ 3 wf        │
-│ design-guidelines   │ 1.0.0   │ main         │ 1 files     │ 3 wf        │
-└─────────────────────┴─────────┴──────────────┴─────────────┴─────────────┘
+┌─────────────────────┬─────────┬──────────┬─────────┬──────────────┬────────┬────────┐
+│ Package             │ Version │ Source   │ Prompts │ Instructions │ Agents │ Skills │
+├─────────────────────┼─────────┼──────────┼─────────┼──────────────┼────────┼────────┤
+│ compliance-rules    │ 1.0.0   │ github   │    2    │      1       │   -    │   1    │
+│ design-guidelines   │ 1.0.0   │ github   │    -    │      1       │   1    │   -    │
+└─────────────────────┴─────────┴──────────┴─────────┴──────────────┴────────┴────────┘
 ```
 
 **Output includes:**
 - Package name and version
-- Source repository/branch information
-- Number of context files (instructions, chatmodes, contexts)
-- Number of agent workflows (prompts)
-- Installation path and status
+- Source information
+- Per-primitive counts (prompts, instructions, agents, skills)
 
 #### `apm deps tree` - 🌳 Show dependency tree structure
 
-Display dependencies in hierarchical tree format showing context and agent workflows.
+Display dependencies in hierarchical tree format with primitive counts.
 
 ```bash
 apm deps tree  

docs/dependencies.md

@@ -45,9 +45,8 @@ Skills are integrated to `.github/skills/`:
 
 | Source | Result |
 |--------|--------|
-| Package with existing `SKILL.md` | Skill folder copied to `.github/skills/{folder-name}/` |
-| APM package with `.apm/` primitives (no SKILL.md) | SKILL.md auto-generated, folder copied to `.github/skills/{folder-name}/` |
-| Package without SKILL.md or primitives | No skill folder created |
+| Package with `SKILL.md` | Skill folder copied to `.github/skills/{folder-name}/` |
+| Package without `SKILL.md` | No skill folder created |
 
 #### Skill Folder Naming
 
@@ -355,6 +354,13 @@ Result:
 - `depth: 1` = direct dependency
 - `depth: 2+` = transitive dependency
 
+Uninstalling a package also removes its orphaned transitive dependencies (npm-style pruning):
+
+```bash
+apm uninstall acme/package-a
+# Also removes B and C if no other package depends on them
+```
+
 ### Cleaning Dependencies
 
 ```bash

docs/integrations.md

@@ -264,9 +264,8 @@ apm install ComposioHQ/awesome-claude-skills/mcp-builder
 **How skill integration works:**
 1. `apm install` checks if the package contains a `SKILL.md` file
 2. If `SKILL.md` exists: copies the entire skill folder to `.github/skills/{folder-name}/`
-3. If no `SKILL.md` but package has `.apm/` primitives: auto-generates `SKILL.md` in `.github/skills/{folder-name}/`
-4. Updates `.gitignore` to exclude generated skills
-5. `apm uninstall` removes the skill folder
+3. Updates `.gitignore` to exclude integrated skills
+4. `apm uninstall` removes the skill folder
 
 ### Target-Specific Compilation
 

docs/skills.md

@@ -275,7 +275,7 @@ APM automatically detects package types:
 | Has | Type | Detection |
 |-----|------|-----------|
 | `apm.yml` only | APM Package | Standard APM primitives |
-| `SKILL.md` only | Claude Skill | Auto-generates `apm.yml` |
+| `SKILL.md` only | Claude Skill | Treated as native skill |
 | Both files | Hybrid Package | Best of both worlds |
 
 ## Target Detection