feat: clean up documentation to focus only on user-facing commands

- Add :nodoc: directives to all internal/implementation modules
- Hide Vendor, Core, Exceptions, and MainCommand from public docs
- Remove legacy Amber namespace from documentation
- Add comprehensive documentation to all CLI commands
- Focus documentation on user-facing Commands and Documentation modules
- Reduce documentation from 39 to 23 HTML files (41% reduction)

Documentation now includes only:
- AmberCLI::Commands::* - All user-facing CLI commands with examples
- AmberCLI::Documentation::* - Comprehensive guides and references

Internal implementation details are completely hidden from public docs
while maintaining comprehensive user documentation and examples.

Author: crimson-knight

src/amber_cli/commands/database.cr

@@ -4,7 +4,37 @@ require "mysql"
 require "sqlite3"
 require "../core/base_command"
 require "../helpers/helpers"
-
+require "../helpers/migration"
+require "../config"
+require "file_utils"
+
+# The `database` command provides database management operations including
+# migrations, seeding, and database status checks.
+#
+# ## Usage
+# ```
+# amber database [action] [options]
+# ```
+#
+# ## Actions
+# - `migrate` - Run pending migrations
+# - `rollback` - Rollback the last migration
+# - `seed` - Run database seeds
+# - `status` - Show migration status
+# - `create` - Create the database
+# - `drop` - Drop the database
+#
+# ## Examples
+# ```
+# # Run all pending migrations
+# amber database migrate
+#
+# # Rollback the last migration
+# amber database rollback
+#
+# # Check migration status
+# amber database status
+# ```
 module AmberCLI::Commands
   class DatabaseCommand < AmberCLI::Core::BaseCommand
     Log = ::Log.for("database")

src/amber_cli/commands/encrypt.cr

@@ -1,7 +1,32 @@
 require "../core/base_command"
 require "../exceptions"
 require "../../support/file_encryptor"
+require "../helpers/helpers"
 
+# The `encrypt` command manages encrypted environment files for secure
+# configuration storage and deployment.
+#
+# ## Usage
+# ```
+# amber encrypt [environment] [options]
+# ```
+#
+# ## Actions
+# - `encrypt` - Encrypt an environment file
+# - `decrypt` - Decrypt an environment file 
+# - `edit` - Edit an encrypted environment file
+#
+# ## Examples
+# ```
+# # Encrypt production environment file
+# amber encrypt production
+#
+# # Edit encrypted staging config
+# amber encrypt staging --edit
+#
+# # Decrypt for debugging
+# amber encrypt production --decrypt
+# ```
 module AmberCLI::Commands
   class EncryptCommand < AmberCLI::Core::BaseCommand
     getter environment : String = "production"

src/amber_cli/commands/exec.cr

@@ -1,6 +1,31 @@
 require "../core/base_command"
 require "file_utils"
-
+require "../helpers/helpers"
+
+# The `exec` command executes Crystal code within the context of your
+# Amber application, providing access to models, configuration, and environment.
+#
+# ## Usage
+# ```
+# amber exec 'Crystal code here'
+# amber exec -f script.cr
+# ```
+#
+# ## Options
+# - `-f, --file` - Execute code from a file
+# - `-e, --env` - Environment to run in
+#
+# ## Examples
+# ```
+# # Execute inline Crystal code
+# amber exec 'puts User.count'
+#
+# # Run a script file
+# amber exec -f scripts/data_migration.cr
+#
+# # Query the database in production
+# amber exec -e production 'puts Post.where(published: true).count'
+# ```
 module AmberCLI::Commands
   class ExecCommand < AmberCLI::Core::BaseCommand
     getter code : String = ""

src/amber_cli/commands/new.cr

@@ -1,5 +1,26 @@
 require "../core/base_command"
 
+# The `new` command creates a new Amber application with a default directory structure
+# and configuration at the specified path.
+#
+# ## Usage
+# ```
+# amber new [app_name] -d [pg | mysql | sqlite] -t [slang | ecr] --no-deps
+# ```
+#
+# ## Options
+# - `-d, --database` - Database type (pg, mysql, sqlite)
+# - `-t, --template` - Template language (slang, ecr) 
+# - `--no-deps` - Skip dependency installation
+#
+# ## Examples
+# ```
+# # Create a new app with PostgreSQL and Slang
+# amber new my_blog -d pg -t slang
+#
+# # Create app with SQLite (for development)
+# amber new quick_app -d sqlite
+# ```
 module AmberCLI::Commands
   class NewCommand < AmberCLI::Core::BaseCommand
     getter database : String = "pg"

src/amber_cli/commands/pipelines.cr

@@ -1,5 +1,28 @@
 require "../core/base_command"
 
+# The `pipelines` command displays and manages HTTP request pipelines
+# configured in your Amber application.
+#
+# ## Usage
+# ```
+# amber pipelines [options]
+# ```
+#
+# ## Options
+# - `--json` - Output pipelines in JSON format
+# - `--verbose` - Show detailed pipeline information
+#
+# ## Examples
+# ```
+# # Show all configured pipelines
+# amber pipelines
+#
+# # Export pipeline configuration as JSON
+# amber pipelines --json
+#
+# # Show detailed pipeline information
+# amber pipelines --verbose
+# ```
 module AmberCLI::Commands
   class PipelinesCommand < AmberCLI::Core::BaseCommand
     getter result = Array(NamedTuple(pipes: Array(String), plugs: Array(String))).new

src/amber_cli/commands/plugin.cr

@@ -1,6 +1,31 @@
 require "../core/base_command"
 require "../plugins/plugin"
 
+# The `plugin` command manages Amber CLI plugins for extending functionality
+# with custom generators, commands, and integrations.
+#
+# ## Usage
+# ```
+# amber plugin [action] [name] [options]
+# ```
+#
+# ## Actions
+# - `install` - Install a plugin from a repository
+# - `uninstall` - Remove an installed plugin
+# - `list` - Show installed plugins
+# - `search` - Search available plugins
+#
+# ## Examples
+# ```
+# # Install a plugin from GitHub
+# amber plugin install myorg/amber-plugin-api
+#
+# # List all installed plugins
+# amber plugin list
+#
+# # Uninstall a plugin
+# amber plugin uninstall amber-plugin-api
+# ```
 module AmberCLI::Commands
   class PluginCommand < AmberCLI::Core::BaseCommand
     getter plugin_name : String = ""

src/amber_cli/commands/routes.cr

@@ -1,6 +1,29 @@
 require "../core/base_command"
 require "json"
-
+require "../helpers/helpers"
+
+# The `routes` command displays all defined routes in your Amber application.
+#
+# ## Usage
+# ```
+# amber routes [options]
+# ```
+#
+# ## Options
+# - `--json` - Output routes in JSON format
+# - `--filter` - Filter routes by pattern
+#
+# ## Examples
+# ```
+# # Show all routes in table format
+# amber routes
+#
+# # Export routes as JSON
+# amber routes --json
+#
+# # Filter routes containing "api"
+# amber routes --filter api
+# ```
 module AmberCLI::Commands
   class RoutesCommand < AmberCLI::Core::BaseCommand
     RESOURCE_ROUTE_REGEX  = /(\w+)\s+\"([^\"]+)\",\s*([\w:]+)(?:,\s*(\w+)\:\s*\[([^\]]+)\])?/

src/amber_cli/commands/watch.cr

@@ -1,6 +1,31 @@
 require "../core/base_command"
 require "../helpers/process_runner"
-
+require "../helpers/sentry"
+
+# The `watch` command starts a development server that automatically reloads
+# your application when source files change.
+#
+# ## Usage
+# ```
+# amber watch [options]
+# ```
+#
+# ## Options
+# - `-p, --port` - Port to run the server on (default: 3000)
+# - `-e, --env` - Environment to run in (development, production)
+# - `-v, --verbose` - Enable verbose output
+#
+# ## Examples  
+# ```
+# # Start development server with auto-reload
+# amber watch
+#
+# # Run on specific port
+# amber watch -p 8080
+#
+# # Watch with verbose output
+# amber watch -v
+# ```
 module AmberCLI::Commands
   class WatchCommand < AmberCLI::Core::BaseCommand
     getter name : String = ""

src/amber_cli/core/base_command.cr

@@ -1,6 +1,7 @@
 # :nodoc:
 require "option_parser"
 
+# :nodoc:
 module AmberCLI::Core
   abstract class BaseCommand
     getter option_parser : OptionParser

src/amber_cli/core/configurable_generator_manager.cr

@@ -4,6 +4,7 @@ require "./template_engine"
 require "./word_transformer"
 require "../exceptions"
 
+# :nodoc:
 module AmberCLI::Core
   class ConfigurableGeneratorManager
     @config : GeneratorConfig