Merge branch 'main' into feat/per-project-hub

Author: ravitemer

CHANGELOG.md

@@ -6,8 +6,31 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
-## [5.12.0] - 2025-07-09
+## [5.13.0] - 2025-07-14
+
+### Added
+
+- **Granular Tool Access for CodeCompanion**: Individual MCP servers and tools now available as separate CodeCompanion function tools
+  - Server groups (e.g., `@github`, `@neovim`) and individual tools (e.g., `@github__create_issue`)
+  - Per-tool auto-approval control from Hub UI
+  - Custom tool combinations through CodeCompanion groups
+  - Eliminates system prompt pollution for better model performance
+
+- **Advanced `edit_file` Tool**: Interactive SEARCH/REPLACE block system with real-time diff preview
+  - Intelligent fuzzy matching and comprehensive feedback for LLM learning
+  - Configurable keybindings and behavior through `builtin_tools.edit_file` config
+  - Extensive test suite with 3000+ test cases
+
+### Enhanced
+
+- **JSON Formatting**: Added `jq` support for prettier configuration file formatting
+- **MCP Tool Prompts**: Improved markdown formatting and structure for better LLM consumption
+
+### Fixed
+
+- **Avante Integration**: Fixed tool input formatting for Gemini model compatibility with `use_ReAct_prompt`
 
+## [5.12.0] - 2025-07-09
 
 ### Enhanced
 - **MCP Registry Migration**: Updated to support mcp-hub v4.0.0 with new MCP Registry system

README.md

@@ -119,6 +119,6 @@ Please read the [CONTRIBUTING.md](CONTRIBUTING.md) guide.
 
 Thanks to:
 
-- [cline/mcp-marketplace](https://github.com/cline/mcp-marketplace) for providing the marketplace api
 - [nui.nvim](https://github.com/MunifTanjim/nui.nvim) for inspiring our text highlighting utilities
+- [ravitemer/mcp-registry](https://github.com/ravitemer/mcp-registry) for providing the marketplace api
 

doc/.vitepress/config.mjs

@@ -97,6 +97,14 @@ export default withMermaid(
           collapsed: false,
           items: [
             { text: "servers.json", link: "/mcp/servers_json" },
+            {
+              text: "Builtin Servers",
+              collapsed: true,
+              items: [
+                { text: "Neovim Server", link: "/mcp/builtin/neovim" },
+                { text: "MCPHub Server", link: "/mcp/builtin/mcphub" },
+              ],
+            },
             {
               text: "Lua MCP Servers",
               collapsed: true,

doc/configuration.md

@@ -33,6 +33,29 @@ All options are optional with sensible defaults. See below for each option in de
 
             --- Plugin specific options-------------------
             native_servers = {}, -- add your custom lua native servers here
+            builtin_tools = {
+                edit_file = {
+                    parser = {
+                        track_issues = true,
+                        extract_inline_content = true,
+                    },
+                    locator = {
+                        fuzzy_threshold = 0.8,
+                        enable_fuzzy_matching = true,
+                    },
+                    ui = {
+                        go_to_origin_on_complete = true,
+                        keybindings = {
+                            accept = ".",
+                            reject = ",",
+                            next = "n",
+                            prev = "p",
+                            accept_all = "ga",
+                            reject_all = "gr",
+                        },
+                    },
+                },
+            },
             ui = {
                 window = {
                     width = 0.8, -- 0-1 (ratio); "50%" (percentage); 50 (raw number)
@@ -257,6 +280,21 @@ Default: `{}`
 
 Define custom Lua native MCP servers that run directly in Neovim without external processes. Each server can provide tools, resources, and prompts. Please see [native servers guide](/mcp/native/index) to create MCP Servers in lua.
 
+### builtin_tools
+
+Default:
+
+```lua
+{
+    builtin_tools = {
+        edit_file = {
+        },
+    },
+}
+```
+
+Configuration options for MCPHub's builtin tools like `edit_file` tool. View complete [Builtin Tools Documentation](/mcp/builtin/neovim) for all available tools and their configuration options.
+
 ### ui
 
 Default:

doc/extensions/codecompanion.md

@@ -1,18 +1,21 @@
 # CodeCompanion Integration
 
 <p>
-<video muted controls src="https://github.com/user-attachments/assets/70181790-e949-4df6-a690-c5d7a212e7d1"></video>
+<video muted controls src="https://github.com/user-attachments/assets/1a10ad50-5832-4627-bcc3-be49e7941105"></video>
 </p>
 
 Add MCP capabilities to [CodeCompanion.nvim](https://github.com/olimorris/codecompanion.nvim) by adding it as an extension. 
 
 ## Features
 
-- Access MCP tools via the `@mcp` tool in the chat buffer.
-- Utilize MCP resources as context variables using the `#` prefix (e.g., `#resource_name`).
-- Execute MCP prompts directly using `/mcp:prompt_name` slash commands.
-- Supports 🖼 images as shown in the demo.
-- Receive real-time updates in CodeCompanion when MCP servers change.
+- **Flexible Tool Access**: Multiple ways to use MCP tools - from broad `@mcp` access to granular individual tools
+- **Server Groups**: Access all tools from a specific server (e.g., `@neovim`, `@github`, `@tree_sitter`)
+- **Individual Tools**: Use specific tools with clear namespacing (e.g., `@neovim__read_file`, `@github__create_issue`)
+- **Custom Tool Groups**: Create your own tool combinations for specific workflows
+- **Resource Variables**: Utilize MCP resources as context variables using the `#` prefix (e.g., `#mcp:resource_name`)
+- **Slash Commands**: Execute MCP prompts directly using `/mcp:prompt_name` slash commands
+- **Rich Media Support**: Supports 🖼 images and other media types as shown in the demo
+- **Real-time Updates**: Automatic updates in CodeCompanion when MCP servers change
 
 ## MCP Hub Extension
 
@@ -24,9 +27,16 @@ require("codecompanion").setup({
     mcphub = {
       callback = "mcphub.extensions.codecompanion",
       opts = {
-        show_result_in_chat = true,  -- Show mcp tool results in chat
-        make_vars = true,            -- Convert resources to #variables
-        make_slash_commands = true,  -- Add prompts as /slash commands
+        -- MCP Tools 
+        make_tools = true,              -- Make individual tools (@server__tool) and server groups (@server) from MCP servers
+        show_server_tools_in_chat = true, -- Show individual tools in chat completion (when make_tools=true)
+        add_mcp_prefix_to_tool_names = false, -- Add mcp__ prefix (e.g `@mcp__github`, `@mcp__neovim__list_issues`)
+        show_result_in_chat = true,      -- Show tool results directly in chat buffer
+        format_tool = nil,               -- function(tool_name:string, tool: CodeCompanion.Agent.Tool) : string Function to format tool names to show in the chat buffer
+        -- MCP Resources
+        make_vars = true,                -- Convert MCP resources to #variables for prompts
+        -- MCP Prompts 
+        make_slash_commands = true,      -- Add MCP prompts as /slash commands
       }
     }
   }
@@ -35,52 +45,128 @@ require("codecompanion").setup({
 
 ## Usage
 
-Once configured, you can interact with MCP Hub within the CodeCompanion chat buffer:
+MCP Hub provides multiple ways to access MCP tools in CodeCompanion, giving you flexibility from broad access to fine-grained control:
 
--   **Tool Access:** Type `@mcp` to add available MCP servers to the system prompt, enabling the LLM to use registered MCP tools.
--   **Resources as Variables:** If `make_vars = true`, MCP resources become available as variables prefixed with `#`. You can include these in your prompts (e.g., `Summarize the issues in #mcp:lsp:get_diagnostics`):
+### Tool Access
 
-*Example: Accessing LSP diagnostics*:
+#### 1. Universal MCP Access (`@mcp`)
+Adds all available MCP servers to the system prompt and provides LLM with `@mcp` tool group which has `use_mcp_tool` and `access_mcp_resource` tools. 
+```
+@{mcp} What files are in the current directory?
+```
 
-![image](https://github.com/user-attachments/assets/fb04393c-a9da-4704-884b-2810ff69f59a)
+#### 2. Server Groups (when `make_tools = true`)
+You can add all the enabled tools from a specific server with server groups. Unlike the `@mcp` group where all the running servers are converted and added to the system prompt, the tools added with server groups are pure function tools and hence depend on model support. The available groups depend on your connected MCP servers:
 
-**Prompts as Slash Commands:** If `make_slash_commands = true`, MCP prompts are available as slash commands (e.g., `/mcp:prompt_name`). Arguments are handled via `vim.ui.input`.
+```
+@{neovim} Read the main.lua file    # All tools from the neovim server will be added as function tools
+@{github} Create an issue           
+@{fetch} Get this webpage           
+```
 
-*Example: Using an MCP prompt via slash command*:
+Server groups are automatically created based on your connected MCP servers when enabled via `make_tools`. Check your MCP Hub UI to see which servers you have connected.
 
-![image](https://github.com/user-attachments/assets/678a06a5-ada9-4bb5-8f49-6e58549c8f32)
+MCPHub includes powerful [builtin servers](/mcp/builtin/neovim) like `@neovim` (file operations, terminal, LSP) and `@mcphub` (server management) that are always available.
 
+#### 3. Individual Tools (when `make_tools = true`)
+You can just provide a single tool from a server for fine-grained functionality. Tool names depend on your connected servers:
+```
+@{neovim__read_file} Show me the config file
+@{fetch__fetch} Get this webpage content
+@{github__create_issue} File a bug report
+```
 
+Use the MCP Hub UI or CodeCompanion's tool completion to discover available tools.
 
+#### 4. Custom Tool Sets
+Create your own tool combinations by mixing MCP tools with existing CodeCompanion tools:
 
-## Auto-Approval
+Example configuration for custom tool groups:
 
-By default, whenever codecompanion calls `use_mcp_tool` or `access_mcp_resource` tool, it shows a confirm dialog with tool name, server name and arguments.
+```lua
+require("codecompanion").setup({
+  strategies = {
+    chat = {
+      tools = {
+        groups = {
+          ["github_pr_workflow"] = {
+            description = "GitHub operations from issue to PR",
+            tools = {
+              -- File operations
+              "neovim__read_multiple_files", "neovim__write_file", "neovim__edit_file",
+              -- GitHub operations
+              "github__list_issues", "github__get_issue", "github__get_issue_comments",
+              "github__create_issue", "github__create_pull_request", "github__get_file_contents",
+              "github__create_or_update_file",  "github__search_code"             
+            },
+          },
+        },
+      },
+    },
+  },
+  extensions = {
+    mcphub = {
+      callback = "mcphub.extensions.codecompanion",
+      opts = {
+        make_tools = true,  -- Required for individual tools
+        -- ... other options
+      }
+    }
+  }
+})
+```
 
-![Image](https://github.com/user-attachments/assets/201a5804-99b6-4284-9351-348899e62467)
 
-### Global Auto-Approval
+Then use your custom groups:
+```
+@{github_pr_workflow} Fix this bug, create tests, and submit a PR with proper documentation
+```
 
-You can set `auto_approve` to `true` to automatically approve all MCP tool calls without user confirmation:
+**Important Notes:**
+- Tool names depend on your connected MCP servers
+- Use MCP Hub UI or Codecompanion's tool completion to see available servers and tools  
+- Tool names follow the pattern `servername__toolname`
+- Mix MCP tools with CodeCompanion's built-in tools (`cmd_runner`, `editor`, `files`, etc.)
+- Each MCP tool can be individually auto-approved for fine-grained control (see Auto-Approval section)
+
+### Resources as Variables
+If `make_vars = true`, MCP resources become available as variables prefixed with `#`:
 
-```lua
-require("mcphub").setup({
-    -- This sets vim.g.mcphub_auto_approve to true by default (can also be toggled from the HUB UI with `ga`)
-    auto_approve = true, 
-})
+```
+Fix diagnostics in the file #{mcp:neovim://diagnostics/buffer}
+Analyze the current buffer #{mcp:neovim:buffer}
 ```
 
-This also sets `vim.g.mcphub_auto_approve` variable to `true`. You can also toggle this option in the MCP Hub UI with `ga` keymap. You can see the current auto approval status in the Hub UI.
+*Example: Accessing LSP diagnostics*:
 
-![Image](https://github.com/user-attachments/assets/64708065-3428-4eb3-82a5-e32d2d1f98c6)
+![image](https://github.com/user-attachments/assets/fb04393c-a9da-4704-884b-2810ff69f59a)
 
-### Fine-Grained Auto-Approval
+### Slash Commands
+If `make_slash_commands = true`, MCP prompts are available as slash commands:
 
-![Image](https://github.com/user-attachments/assets/131bfed2-c4e7-4e2e-ba90-c86e6ca257fd)
+```
+/mcp:code_review
+/mcp:explain_function
+/mcp:generate_tests
+```
 
-![Image](https://github.com/user-attachments/assets/befd1d44-bca3-41f6-a99a-3d15c6c8a5f5)
+*Example: Using an MCP prompt via slash command*:
+
+![image](https://github.com/user-attachments/assets/678a06a5-ada9-4bb5-8f49-6e58549c8f32)
+
+
+
+## Auto-Approval
 
-For more control, configure auto-approval per server or per tool in your `servers.json`:
+By default, whenever codecompanion calls `use_mcp_tool` or `access_mcp_resource` tool or a specific tool on some MCP server, it shows a confirm dialog with tool name, server name and arguments.
+
+![Image](https://github.com/user-attachments/assets/201a5804-99b6-4284-9351-348899e62467)
+
+
+#### Fine-Grained Auto-Approval
+
+
+For fine-grained control, configure auto-approval per server or per tool in your `servers.json`:
 
 ```json
 {
@@ -104,7 +190,26 @@ You can also toggle auto-approval from the Hub UI:
 - Press `a` on an individual tool to toggle auto-approval for just that tool
 - Resources are always auto-approved (no configuration needed)
 
-### Function-Based Auto-Approval
+![Image](https://github.com/user-attachments/assets/131bfed2-c4e7-4e2e-ba90-c86e6ca257fd)
+
+![Image](https://github.com/user-attachments/assets/befd1d44-bca3-41f6-a99a-3d15c6c8a5f5)
+
+#### Global Auto-Approval
+
+You can set `auto_approve` to `true` to automatically approve all MCP tool calls without user confirmation:
+
+```lua
+require("mcphub").setup({
+    -- This sets vim.g.mcphub_auto_approve to true by default (can also be toggled from the HUB UI with `ga`)
+    auto_approve = true, 
+})
+```
+
+This also sets `vim.g.mcphub_auto_approve` variable to `true`. You can also toggle this option in the MCP Hub UI with `ga` keymap. You can see the current auto approval status in the Hub UI.
+
+![Image](https://github.com/user-attachments/assets/64708065-3428-4eb3-82a5-e32d2d1f98c6)
+
+#### Function-Based Auto-Approval
 
 For maximum control, provide a function that decides approval based on the specific tool call:
 
@@ -158,13 +263,9 @@ require("mcphub").setup({
 - `string` - Deny with error message
 - `nil` - Show confirmation prompt (same as false)
 
-### Auto-Approval Priority
+#### Auto-Approval Priority
 
 The system checks auto-approval in this order:
 1. **Function**: Custom `auto_approve` function (if provided)
 2. **Server-specific**: `autoApprove` field in server config
 3. **Default**: Show confirmation dialog
-
-
-
-

doc/index.md

@@ -83,6 +83,15 @@ Just configure them to use MCP Hub's unified endpoint:
 - Toggle servers, tools, and resources etc
 - Test tools and resources directly in Neovim
 
+### Builtin Native Servers
+
+MCPHub includes two native servers that run directly within Neovim:
+
+- **Neovim Server**: Comprehensive file operations, terminal access, LSP integration, and buffer management
+- **MCPHub Server**: Plugin management utilities, server lifecycle control, and documentation access
+
+These servers provide essential functionality without external dependencies and offer deep Neovim integration.
+
 ### Chat Integrations
 
 - MCP Hub provides integrations with popular chat plugins like [Avante](https://github.com/yetone/avante.nvim), [CodeCompanion](https://github.com/olimorris/codecompanion.nvim), [CopilotChat](https://github.com/CopilotC-Nvim/CopilotChat.nvim).
@@ -131,8 +140,3 @@ Just configure them to use MCP Hub's unified endpoint:
 
 - [Installation Guide](/installation) - Set up MCPHub in your Neovim
 - [Configuration Guide](/configuration) - Learn about configuring MCP Hub
-
-
-
-
-