Add configuration file support and fix SSE notifications

.vscode/launch.json

@@ -17,91 +17,7 @@
             "request": "launch",
             "mode": "auto",
             "program": "${workspaceFolder}/cmd/go-go-mcp",
-            "args": ["start", "--transport", "sse", "--repositories", "examples/prompto", "--log-level", "debug", "--port", "3000"],
-            "cwd": "${workspaceFolder}"
-        },
-        {
-            "name": "Simplify HTML",
-            "type": "go",
-            "request": "launch",
-            "mode": "auto",
-            "program": "${workspaceFolder}/cmd/tools/simplify-html",
-            "args": ["simplify", "--files", "/tmp/foxp3.html", "--max-list-items", "5"],
-            "cwd": "${workspaceFolder}"
-        },
-        {
-            "name": "Test HTML Selector",
-            "type": "go",
-            "request": "launch",
-            "mode": "auto",
-            "program": "${workspaceFolder}/cmd/tools/test-html-selector",
-            "args": [
-                "select",
-                "--config",
-                "cmd/tools/test-html-selector/examples/tutorial/01-basic-text.yaml",
-                "--files",
-                "cmd/tools/test-html-selector/examples/tutorial/01-basic-text.html"
-            ],
-            "cwd": "${workspaceFolder}"
-        },
-        {
-            "name": "Test HTML Selector - PubMed FOXP3",
-            "type": "go",
-            "request": "launch",
-            "mode": "auto",
-            "program": "${workspaceFolder}/cmd/tools/test-html-selector",
-            "args": [
-                "select",
-                "--config",
-                "cmd/tools/test-html-selector/examples/pubmed.yaml",
-                "--urls",
-                "https://pubmed.ncbi.nlm.nih.gov/?term=foxp3",
-                "--extract"
-            ],
-            "cwd": "${workspaceFolder}"
-        },
-        {
-            "name": "Run HTML Extract - HN",
-            "type": "go",
-            "request": "launch",
-            "mode": "auto",
-            "program": "${workspaceFolder}/cmd/go-go-mcp",
-            "args": ["run-command", "examples/html-extract/fetch-html.yaml", "--urls", "https://news.ycombinator.com/"],
-            "cwd": "${workspaceFolder}"
-        },
-        {
-            "name": "HTML Selector - CSS Select",
-            "type": "go",
-            "request": "launch",
-            "mode": "auto",
-            "program": "${workspaceFolder}/cmd/tools/test-html-selector",
-            "args": [
-                "select",
-                "--files",
-                "hn.html",
-                "--log-level",
-                "DEBUG",
-                "--select-css",
-                "td.title"
-            ],
-            "cwd": "${workspaceFolder}"
-        },
-        {
-            "name": "HTML Selector - Config File",
-            "type": "go",
-            "request": "launch",
-            "mode": "auto",
-            "program": "${workspaceFolder}/cmd/tools/test-html-selector",
-            "args": [
-                "select",
-                "--files",
-                "hn.html",
-                "--log-level",
-                "DEBUG",
-                "--show-simplified",
-                "--config",
-                "/tmp/html-extraction-2025-01-26-18-20-00.yaml"
-            ],
+            "args": ["start", "--transport", "sse", "--profile", "all", "--log-level", "debug", "--port", "3000"],
             "cwd": "${workspaceFolder}"
         }
     ]

Makefile

@@ -47,6 +47,7 @@ bump-glazed:
 	go get github.com/go-go-golems/glazed@latest
 	go get github.com/go-go-golems/clay@latest
 	go get github.com/go-go-golems/geppetto@latest
+	go get github.com/go-go-golems/parka@latest
 	go mod tidy
 
 go-go-mcp_BINARY=$(shell which go-go-mcp)

README.md

@@ -2,6 +2,44 @@
 
 A Go implementation of the Model Context Protocol (MCP), providing a framework for building MCP servers and clients.
 
+### Installation
+
+To install the `go-go-mcp` command line tool with homebrew, run:
+
+```bash
+brew tap go-go-golems/go-go-go
+brew install go-go-golems/go-go-go/go-go-mcp
+```
+
+To install the `go-go-mcp` command using apt-get, run:
+
+```bash
+echo "deb [trusted=yes] https://apt.fury.io/go-go-golems/ /" >> /etc/apt/sources.list.d/fury.list
+apt-get update
+apt-get install go-go-mcp
+```
+
+To install using `yum`, run:
+
+```bash
+echo "
+[fury]
+name=Gemfury Private Repo
+baseurl=https://yum.fury.io/go-go-golems/
+enabled=1
+gpgcheck=0
+" >> /etc/yum.repos.d/fury.repo
+yum install go-go-mcp
+```
+
+To install using `go get`, run:
+
+```bash
+go get -u github.com/go-go-golems/go-go-mcp/cmd/go-go-mcp
+```
+
+Finally, install by downloading the binaries straight from [github](https://github.com/go-go-golems/go-go-mcp/releases).
+
 ## Overview
 
 This project implements the [Model Context Protocol](https://github.com/modelcontextprotocol/specification), which enables standardized communication between AI applications and language models. The implementation includes:
@@ -154,10 +192,10 @@ Start the server with either stdio or SSE transport:
 
 ```bash
 # Start with stdio transport (default)
-./go-go-mcp start --transport stdio
+go-go-mcp start --transport stdio
 
 # Start with SSE transport
-./go-go-mcp start --transport sse --port 3001
+go-go-mcp start --transport sse --port 3001
 ```
 
 #### Client Mode
@@ -166,26 +204,26 @@ Use the client subcommand to interact with an MCP server:
 
 ```bash
 # List available prompts (uses default server: go-go-mcp start --transport stdio)
-./go-go-mcp client prompts list
+go-go-mcp client prompts list
 
 # List available tools
-./go-go-mcp client tools list
+go-go-mcp client tools list
 
 # Execute a prompt with arguments
-./go-go-mcp client prompts execute hello --args '{"name":"World"}'
+go-go-mcp client prompts execute hello --args '{"name":"World"}'
 
 # Call a tool with arguments
-./go-go-mcp client tools call echo --args '{"message":"Hello, MCP!"}'
+go-go-mcp client tools call echo --args '{"message":"Hello, MCP!"}'
 ```
 
 You can customize the server command and arguments if needed:
 
 ```bash
 # Use a different server binary with custom arguments
-./go-go-mcp client --command custom-server,start,--debug,--port,8001 prompts list
+go-go-mcp client --command custom-server,start,--debug,--port,8001 prompts list
 
 # Use a server with a specific configuration
-./go-go-mcp client -c go-go-mcp,start,--config,config.yaml prompts list
+go-go-mcp client -c go-go-mcp,start,--config,config.yaml prompts list
 ```
 
 #### Using SSE Transport
@@ -194,52 +232,158 @@ For web-based applications, use the SSE transport:
 
 ```bash
 # Start the server with SSE transport
-./go-go-mcp start --transport sse --port 3001
+go-go-mcp start --transport sse --port 3001
 
 # In another terminal, connect using the client
-./go-go-mcp client --transport sse --server http://localhost:3001 prompts list
+go-go-mcp client --transport sse --server http://localhost:3001 prompts list
 ```
 
+#### Using go-go-mcp as a Bridge
+
+go-go-mcp can be used as a bridge to expose an SSE server as a stdio server. This is useful when you need to connect a stdio-based client to an SSE server:
+
+```bash
+# Start an SSE server on port 3000
+go-go-mcp start --transport sse --port 3000
+
+# In another terminal, start the bridge to expose the SSE server as stdio
+go-go-mcp bridge --sse-url http://localhost:3000 --log-level debug
+
+# Now you can use stdio-based clients to connect to the bridge
+```
+
+This is particularly useful when integrating with tools that only support stdio communication but need to connect to a web-based MCP server.
+
 ### Debug Mode
 
 Add the `--debug` flag to enable detailed logging:
 
 ```bash
-./go-go-mcp client --debug prompts list
+go-go-mcp client --debug prompts list
 ```
 
 ### Version Information
 
 Check the version:
 
 ```bash
-./go-go-mcp version
+go-go-mcp version
 ```
 
-### Project Structure
+## Configuration
 
-- `pkg/`
-  - `protocol/` - Core protocol types and interfaces
-  - `prompts/` - Prompt registry and handlers
-  - `resources/` - Resource registry and handlers
-  - `tools/` - Tool registry and handlers
-  - `server/` - Server implementation
-  - `doc/` - Documentation
-- `cmd/`
-  - `mcp-server/` - MCP server and client implementation
-    - `cmds/` - Command implementations
-      - `client/` - Client subcommands
+go-go-mcp can be configured using YAML configuration files that allow you to:
+- Define multiple profiles for different environments
+- Configure tool and prompt sources
+- Set parameter defaults and overrides
+- Control access through blacklists/whitelists
+- Manage security through parameter filtering
 
-### Dependencies
+For detailed configuration documentation, use:
+```bash
+# View configuration file documentation
+go-go-mcp help config-file
+
+# View example configuration
+go-go-mcp help config-file --example
+```
+
+## Shell Commands
+
+go-go-mcp supports defining custom shell commands in YAML files, providing:
+- Template-based command generation with Go templates and Sprig functions
+- Rich parameter type system
+- Environment variable management
+- Working directory control
+- Error handling and output capture
 
-- `github.com/rs/zerolog` - Structured logging
-- `github.com/spf13/cobra` - Command-line interface
-- Standard Go libraries
+### Example Commands
+
+The `examples/` directory contains various ready-to-use commands. You can view the schema for any command using `go-go-mcp schema <command.yaml>`, which shows the full parameter documentation that is passed to the LLM:
+
+```bash
+go-go-mcp schema examples/github/list-github-issues.yaml
+```
 
-## Contributing
+#### GitHub Integration
+- [`examples/github/list-github-issues.yaml`](examples/github/list-github-issues.yaml) - List and filter GitHub issues
+- [`examples/github/list-pull-requests.yaml`](examples/github/list-pull-requests.yaml) - List and filter pull requests
 
-Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.
+#### Web Content Tools
+- [`examples/shell-commands/fetch-url.yaml`](examples/shell-commands/fetch-url.yaml) - Fetch and process web content
+- [`examples/html-extract/pubmed.yaml`](examples/html-extract/pubmed.yaml) - Search and extract data from PubMed
 
-## License
+#### Research and Documentation
+- [`examples/shell-commands/diary-append.yaml`](examples/shell-commands/diary-append.yaml) - Maintain a timestamped diary
+- [`examples/shell-commands/fetch-transcript.yaml`](examples/shell-commands/fetch-transcript.yaml) - Download YouTube video transcripts
 
-[Insert your chosen license here]
+For any command, you can view its full schema and documentation using:
+```bash
+# View the full parameter schema and documentation
+go-go-mcp schema examples/github/list-github-issues.yaml
+
+# View the command help
+go-go-mcp run-command examples/github/list-github-issues.yaml --help
+```
+
+### Running Shell Commands Directly
+
+You can run shell commands directly using the `run-command` subcommand. This allows you to execute any shell command YAML file without loading it into a server first:
+
+```bash
+# View command help and available flags
+go-go-mcp run-command examples/github/list-github-issues.yaml --help
+
+# Run a command with specific parameters
+go-go-mcp run-command examples/github/list-github-issues.yaml --author wesen
+
+# Run a Google Calendar command
+go-go-mcp run-command examples/google/get-calendar.yaml --start today --end "next week"
+
+# Run a URL fetching command
+go-go-mcp run-command examples/shell-commands/fetch-url.yaml --url https://example.com
+```
+
+This provides a simpler way to use shell commands as standalone command-line tools without setting up a server.
+
+### Generating Shell Commands with Pinocchio
+
+You can use [Pinocchio](https://github.com/go-go-golems/pinocchio) to generate shell commands for go-go-mcp. First, add your local go-go-mcp repository as a Pinocchio repository:
+
+```bash
+pinocchio config repositories add $(pwd)/pinocchio
+```
+
+Then generate a new command using:
+
+```bash
+pinocchio go-go-mcp create-command --description "A command description"
+```
+
+This will create a new shell command YAML file with the appropriate structure and configuration.
+
+For detailed shell commands documentation, use:
+```bash
+# View shell commands documentation
+go-go-mcp help shell-commands
+
+# View example shell commands
+go-go-mcp help shell-commands --example
+```
+
+## Help System
+
+go-go-mcp comes with comprehensive built-in documentation. To explore:
+
+```bash
+# List all available help topics
+go-go-mcp help --all
+
+# Get help on a specific topic
+go-go-mcp help <topic>
+
+# Show examples for a topic
+go-go-mcp help <topic> --example
+```
+
+### Project Structure