Update documentation with missing features and fix broken links

- Fix 10 broken documentation links (now point to docs/reference/)
- Add CLI commands for Registry, Collections, Project Dependencies, Config
- Add Project Dependencies section (cmdforge.yaml manifest)
- Add Collections section (curated tool bundles)
- Add Registry section (search, publish, moderation status)
- Add Tool Documentation section (cmdforge docs command)
- Update wiki with Collections, Registry, and Project Dependencies

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

README.md

@@ -94,7 +94,7 @@ pip install -e ".[dev]"
 ### Requirements
 
 - Python 3.10+
-- At least one AI CLI tool installed (see [Provider Setup](docs/PROVIDERS.md))
+- At least one AI CLI tool installed (see [Provider Setup](docs/reference/providers.md))
 - PySide6 (included automatically - requires display server on Linux)
 
 ### Post-Install
@@ -127,6 +127,7 @@ Opens the graphical interface where you can create and manage tools visually. Fe
 ### CLI Mode
 
 ```bash
+# Tool Management
 cmdforge list              # List all tools
 cmdforge create mytool     # Create new tool
 cmdforge edit mytool       # Edit in $EDITOR
@@ -135,6 +136,30 @@ cmdforge run mytool        # Run a tool
 cmdforge test mytool       # Test with mock provider
 cmdforge check mytool      # Check dependencies (meta-tools)
 cmdforge refresh           # Update executable wrappers
+cmdforge docs mytool       # View/create tool documentation
+
+# Registry
+cmdforge registry search "keyword"    # Search for tools
+cmdforge registry install owner/tool  # Install a tool
+cmdforge registry publish mytool      # Publish your tool
+cmdforge registry status              # Check moderation status
+cmdforge registry my-tools            # List your published tools
+
+# Collections (curated tool bundles)
+cmdforge collections list             # List available collections
+cmdforge collections info starter     # View collection details
+cmdforge collections install starter  # Install all tools in a collection
+
+# Project Dependencies
+cmdforge init                         # Create cmdforge.yaml manifest
+cmdforge add owner/tool               # Add tool as dependency
+cmdforge install                      # Install all dependencies
+cmdforge deps                         # Check dependency status
+
+# Configuration
+cmdforge config show                  # Show current config
+cmdforge config connect username      # Connect to registry account
+cmdforge config disconnect            # Disconnect from registry
 ```
 
 ### Running Tools
@@ -282,7 +307,7 @@ CmdForge works with any AI CLI tool. We've profiled 12 providers:
 | `claude-opus` | 18s | 4/4 | $$$ | Highest quality |
 | `gemini` | 91s | 3/4 | Paid | Large docs (1M tokens) |
 
-See [docs/PROVIDERS.md](docs/PROVIDERS.md) for setup instructions.
+See [Provider Setup](docs/reference/providers.md) for setup instructions.
 
 ## Tool Anatomy
 
@@ -374,7 +399,7 @@ output: "{translated}"
 
 Check dependencies before running: `cmdforge check my-meta-tool`
 
-See [docs/META_TOOLS.md](docs/META_TOOLS.md) for full documentation.
+See [Meta-Tools Design](docs/reference/meta-tools.md) for full documentation.
 
 ### Variables
 
@@ -384,6 +409,125 @@ See [docs/META_TOOLS.md](docs/META_TOOLS.md) for full documentation.
 | `{argname}` | Custom argument value |
 | `{output_var}` | Output from previous step (prompt, code, or tool) |
 
+## Project Dependencies
+
+For projects that use multiple CmdForge tools, you can declare dependencies in a `cmdforge.yaml` manifest:
+
+```yaml
+# cmdforge.yaml
+name: my-project
+description: My awesome project
+dependencies:
+  - official/summarize
+  - official/translate
+  - myuser/custom-tool@^1.0.0
+```
+
+### Managing Dependencies
+
+```bash
+# Initialize a new manifest
+cmdforge init
+
+# Add a dependency
+cmdforge add official/summarize
+cmdforge add myuser/tool@^2.0.0    # With version constraint
+
+# Install all dependencies
+cmdforge install
+
+# Check dependency status
+cmdforge deps
+```
+
+This ensures all required tools are available before running your project's scripts.
+
+## Collections
+
+Collections are curated bundles of related tools. Install an entire workflow with one command:
+
+```bash
+# List available collections
+cmdforge collections list
+
+# View what's in a collection
+cmdforge collections info starter
+# Output:
+#   starter - Essential tools for getting started
+#   Tools: summarize, translate, fix-grammar, explain-error, commit-msg
+#   Total: 5 tools
+
+# Install all tools in a collection
+cmdforge collections install starter
+```
+
+### Available Collections
+
+| Collection | Description | Tools |
+|------------|-------------|-------|
+| `starter` | Essential tools for beginners | 5 |
+| `developer` | Code review and development | 8 |
+| `writer` | Writing and editing tools | 6 |
+| `data` | Data extraction and conversion | 7 |
+
+## Registry
+
+The CmdForge Registry at [cmdforge.brrd.tech](https://cmdforge.brrd.tech) hosts community tools.
+
+### Searching Tools
+
+```bash
+# Basic search
+cmdforge registry search "summarize"
+
+# Filter by category
+cmdforge registry search --category Developer
+
+# Sort by popularity
+cmdforge registry search --sort downloads
+
+# Show only new tools (last 7 days)
+cmdforge registry search --new
+
+# Advanced filters
+cmdforge registry search --owner official --min-downloads 100
+```
+
+### Publishing Tools
+
+```bash
+# Connect your account (opens browser for authentication)
+cmdforge config connect yourusername
+
+# Publish a tool
+cmdforge registry publish mytool
+
+# Check moderation status
+cmdforge registry status
+# Output:
+#   mytool: pending (submitted 2 hours ago)
+#   other-tool: approved
+
+# Sync moderation feedback to your local tool
+cmdforge registry status --sync
+```
+
+Published tools go through moderation before appearing publicly. You'll receive feedback if changes are requested.
+
+### Tool Documentation
+
+Each tool can have its own README:
+
+```bash
+# View tool documentation
+cmdforge docs mytool
+
+# Create/edit documentation (opens in $EDITOR)
+cmdforge docs mytool --edit
+```
+
+The documentation is stored as `README.md` in the tool's directory (`~/.cmdforge/mytool/README.md`).
+
 ## Shell Integration
 
 ### Git Hooks
@@ -668,16 +812,14 @@ cmdforge providers test claude
 ## Links
 
 ### User Documentation
-- [Installation Guide](docs/INSTALL.md)
+- [Provider Setup](docs/reference/providers.md)
-- [Provider Setup](docs/PROVIDERS.md)
+- [Example Tools](docs/reference/examples.md)
-- [Example Tools](docs/EXAMPLES.md)
 - [User Wiki](wiki/Home.md)
 
 ### Developer Documentation
-- [Project Overview](docs/PROJECT.md) - Start here to understand the codebase
+- [Project Overview](docs/overview.md) - Start here to understand the codebase
-- [Design Document](docs/DESIGN.md)
+- [Design Document](docs/reference/design.md)
-- [Meta-Tools Design](docs/META_TOOLS.md) - Tools that call other tools
+- [Meta-Tools Design](docs/reference/meta-tools.md) - Tools that call other tools
-- [Registry API Design](docs/REGISTRY.md)
+- [Collections](docs/reference/collections.md) - Curated tool bundles
-- [Web UI Design](docs/WEB_UI.md)
+- [Registry API Design](docs/reference/registry-spec.md)
-- [Deployment Guide](docs/DEPLOYMENT.md)
+- [Web UI Design](docs/reference/web-ui-spec.md)
-- [Architecture Diagrams](docs/diagrams/)

wiki/Home.md

@@ -342,9 +342,96 @@ git diff --stat | awk '$3 > 100 {print $1}' | xargs cat | review-code
 
 ---
 
+## Collections
+
+Collections are curated bundles of related tools. Get started quickly by installing a whole workflow:
+
+```bash
+# See available collections
+cmdforge collections list
+
+# Learn what's in a collection
+cmdforge collections info starter
+
+# Install all tools in a collection
+cmdforge collections install starter
+```
+
+### Popular Collections
+
+| Collection | What you get |
+|------------|--------------|
+| `starter` | summarize, translate, fix-grammar, explain-error, commit-msg |
+| `developer` | Code review, test generation, error explanation |
+| `writer` | Grammar, tone, simplification, expansion tools |
+| `data` | JSON extraction, CSV conversion, data analysis |
+
+---
+
+## Registry
+
+The [CmdForge Registry](https://cmdforge.brrd.tech) hosts community-created tools.
+
+### Finding Tools
+
+```bash
+# Search by keyword
+cmdforge registry search "code review"
+
+# Browse by category
+cmdforge registry search --category Developer
+
+# Find popular tools
+cmdforge registry search --sort downloads --popular
+
+# Install a tool
+cmdforge registry install official/summarize
+```
+
+### Publishing Your Tools
+
+Share your tools with the community:
+
+```bash
+# Connect to your registry account
+cmdforge config connect yourusername
+# (Opens browser for authentication)
+
+# Publish a tool
+cmdforge registry publish mytool
+
+# Check status (tools are moderated)
+cmdforge registry status
+```
+
+---
+
+## Project Dependencies
+
+For projects using multiple tools, create a `cmdforge.yaml` manifest:
+
+```yaml
+name: my-project
+dependencies:
+  - official/summarize
+  - official/translate
+```
+
+Then manage dependencies:
+
+```bash
+cmdforge init          # Create manifest
+cmdforge add tool      # Add dependency
+cmdforge install       # Install all
+cmdforge deps          # Check status
+```
+
+---
+
 ## Links
 
 - **Repository**: https://gitea.brrd.tech/rob/CmdForge
+- **Registry**: https://cmdforge.brrd.tech
 - **Docker Image**: `gitea.brrd.tech/rob/cmdforge:latest`
 - **Issues**: https://gitea.brrd.tech/rob/CmdForge/issues