Merge branch 'main' into add-issue-dependencies

Author: eshaffer321

.github/copilot-instructions.md

@@ -243,7 +243,6 @@ All workflows run on push/PR unless noted. Located in `.github/workflows/`:
 - **GITHUB_HOST** - For GitHub Enterprise Server (prefix with `https://`)
 - **GITHUB_TOOLSETS** - Comma-separated toolset list (overrides --toolsets flag)
 - **GITHUB_READ_ONLY** - Set to "1" for read-only mode
-- **GITHUB_DYNAMIC_TOOLSETS** - Set to "1" for dynamic toolset discovery
 - **UPDATE_TOOLSNAPS** - Set to "true" when running tests to update snapshots
 - **GITHUB_MCP_SERVER_E2E_TOKEN** - Token for e2e tests
 - **GITHUB_MCP_SERVER_E2E_DEBUG** - Set to "true" for in-process e2e debugging
@@ -273,7 +272,7 @@ server.json         - MCP server registry metadata
 `cmd/github-mcp-server/main.go` - Uses cobra for CLI, viper for config, supports:
 - `stdio` command (default) - MCP stdio transport
 - `generate-docs` command - Documentation generation
-- Flags: --toolsets, --read-only, --dynamic-toolsets, --gh-host, --log-file
+- Flags: --toolsets, --read-only, --gh-host, --log-file
 
 ## Important Reminders
 

.github/workflows/mcp-diff.yml

@@ -34,8 +34,6 @@ jobs:
             [
               {"name": "default", "args": ""},
               {"name": "read-only", "args": "--read-only"},
-              {"name": "dynamic-toolsets", "args": "--dynamic-toolsets"},
-              {"name": "read-only+dynamic", "args": "--read-only --dynamic-toolsets"},
               {"name": "toolsets-repos", "args": "--toolsets=repos"},
               {"name": "toolsets-issues", "args": "--toolsets=issues"},
               {"name": "toolsets-context", "args": "--toolsets=context"},
@@ -45,20 +43,7 @@ jobs:
               {"name": "toolsets-all", "args": "--toolsets=all"},
               {"name": "tools-get_me", "args": "--tools=get_me"},
               {"name": "tools-get_me,list_issues", "args": "--tools=get_me,list_issues"},
-              {"name": "toolsets-repos+read-only", "args": "--toolsets=repos --read-only"},
-              {"name": "toolsets-all+dynamic", "args": "--toolsets=all --dynamic-toolsets"},
-              {"name": "toolsets-repos+dynamic", "args": "--toolsets=repos --dynamic-toolsets"},
-              {"name": "toolsets-repos,issues+dynamic", "args": "--toolsets=repos,issues --dynamic-toolsets"},
-              {
-                "name": "dynamic-tool-calls",
-                "args": "--dynamic-toolsets",
-                "custom_messages": [
-                  {"id": 10, "name": "list_toolsets_before", "message": {"jsonrpc": "2.0", "id": 10, "method": "tools/call", "params": {"name": "list_available_toolsets", "arguments": {}}}},
-                  {"id": 11, "name": "get_toolset_tools", "message": {"jsonrpc": "2.0", "id": 11, "method": "tools/call", "params": {"name": "get_toolset_tools", "arguments": {"toolset": "repos"}}}},
-                  {"id": 12, "name": "enable_toolset", "message": {"jsonrpc": "2.0", "id": 12, "method": "tools/call", "params": {"name": "enable_toolset", "arguments": {"toolset": "repos"}}}},
-                  {"id": 13, "name": "list_toolsets_after", "message": {"jsonrpc": "2.0", "id": 13, "method": "tools/call", "params": {"name": "list_available_toolsets", "arguments": {}}}}
-                ]
-              }
+              {"name": "toolsets-repos+read-only", "args": "--toolsets=repos --read-only"}
             ]
 
       - name: Add interpretation note

README.md

@@ -424,7 +424,7 @@ The environment variable `GITHUB_TOOLSETS` takes precedence over the command lin
 
 #### Specifying Individual Tools
 
-You can also configure specific tools using the `--tools` flag. Tools can be used independently or combined with toolsets and dynamic toolsets discovery for fine-grained control.
+You can also configure specific tools using the `--tools` flag. Tools can be used independently or combined with toolsets for fine-grained control.
 
 1. **Using Command Line Argument**:
 
@@ -446,17 +446,9 @@ You can also configure specific tools using the `--tools` flag. Tools can be use
 
    This registers all tools from `repos` and `issues` toolsets, plus `get_gist`.
 
-4. **Combining with Dynamic Toolsets** (additive):
-
-   ```bash
-   github-mcp-server --tools get_file_contents --dynamic-toolsets
-   ```
-
-   This registers `get_file_contents` plus the dynamic toolset tools (`enable_toolset`, `list_available_toolsets`, `get_toolset_tools`).
-
 **Important Notes:**
 
-- Tools, toolsets, and dynamic toolsets can all be used together
+- Tools and toolsets can be used together
 - Read-only mode takes priority: write tools are skipped if `--read-only` is set, even if explicitly requested via `--tools`
 - Tool names must match exactly (e.g., `get_file_contents`, not `getFileContents`). Invalid tool names will cause the server to fail at startup with an error message
 - When tools are renamed, old names are preserved as aliases for backward compatibility. See [Tool Renaming](docs/tool-renaming.md) for details.
@@ -657,6 +649,8 @@ The following sets of tools are available:
   - **Required OAuth Scopes**: `security_events`
   - **Accepted OAuth Scopes**: `repo`, `security_events`
   - `owner`: The owner of the repository. (string, required)
+  - `page`: Page number for pagination (min 1) (number, optional)
+  - `perPage`: Results per page for pagination (min 1, max 100) (number, optional)
   - `ref`: The Git reference for the results you want to list. (string, optional)
   - `repo`: The name of the repository. (string, required)
   - `severity`: Filter code scanning alerts by severity (string, optional)
@@ -720,6 +714,8 @@ The following sets of tools are available:
   - **Required OAuth Scopes**: `security_events`
   - **Accepted OAuth Scopes**: `repo`, `security_events`
   - `owner`: The owner of the repository. (string, required)
+  - `page`: Page number for pagination (min 1) (number, optional)
+  - `perPage`: Results per page for pagination (min 1, max 100) (number, optional)
   - `repo`: The name of the repository. (string, required)
   - `severity`: Filter dependabot alerts by severity (string, optional)
   - `state`: Filter dependabot alerts by state. Defaults to open (string, optional)
@@ -1135,6 +1131,7 @@ The following sets of tools are available:
 
 - **pull_request_read** - Get details for a single pull request
   - **Required OAuth Scopes**: `repo`
+  - `after`: Cursor for pagination, used only by the get_review_comments method. Pass the endCursor from the previous page's PageInfo to fetch the next page. (string, optional)
   - `method`: Action to specify what pull request data needs to be retrieved from GitHub. 
     Possible options: 
      1. get - Get details of a specific pull request.
@@ -1326,9 +1323,17 @@ The following sets of tools are available:
   - `order`: Sort order for results (string, optional)
   - `page`: Page number for pagination (min 1) (number, optional)
   - `perPage`: Results per page for pagination (min 1, max 100) (number, optional)
-  - `query`: Search query using GitHub's powerful code search syntax. Examples: 'content:Skill language:Java org:github', 'NOT is:archived language:Python OR language:go', 'repo:github/github-mcp-server'. Supports exact matching, language filters, path filters, and more. (string, required)
+  - `query`: Search query (GitHub code search REST). Implicit AND between terms; supports `OR`, `NOT`, and `"quoted phrase"` for exact match. Qualifiers: `repo:owner/repo`, `org:`, `user:`, `language:`, `path:dir` (prefix match), `filename:exact.ext`, `extension:`, `in:file`, `in:path`, `size:`, `is:archived`, `is:fork`. Max 256 chars. Examples: `WithContext language:go org:github`; `"package main" repo:o/r`; `func extension:go path:cmd repo:o/r`; `NOT TODO language:go repo:o/r`. (string, required)
   - `sort`: Sort field ('indexed' only) (string, optional)
 
+- **search_commits** - Search commits
+  - **Required OAuth Scopes**: `repo`
+  - `order`: Sort order (string, optional)
+  - `page`: Page number for pagination (min 1) (number, optional)
+  - `perPage`: Results per page for pagination (min 1, max 100) (number, optional)
+  - `query`: Commit search query (GitHub commit search REST). Searches commit messages on the default branch only. Scope the search with `repo:owner/repo`, `org:`, or `user:` (queries without a scope qualifier match across all of GitHub and are usually not what you want). Other qualifiers: `author:`, `committer:`, `author-name:`, `committer-name:`, `author-email:`, `committer-email:`, `author-date:`, `committer-date:` (supports `>`, `<`, `>=`, `<=`, and `YYYY-MM-DD..YYYY-MM-DD` ranges), `merge:true|false`, `hash:`, `tree:`, `parent:`, `is:public`. Examples: `repo:owner/repo fix panic`; `org:github author:defunkt committer-date:>=2024-01-01`; `"refactor cache" repo:o/r`; `hash:abc1234 repo:o/r`. (string, required)
+  - `sort`: Sort by author or committer date (defaults to best match) (string, optional)
+
 - **search_repositories** - Search repositories
   - **Required OAuth Scopes**: `repo`
   - `minimal_output`: Return minimal repository information (default: true). When false, returns full GitHub API repository objects. (boolean, optional)
@@ -1355,6 +1360,8 @@ The following sets of tools are available:
   - **Required OAuth Scopes**: `security_events`
   - **Accepted OAuth Scopes**: `repo`, `security_events`
   - `owner`: The owner of the repository. (string, required)
+  - `page`: Page number for pagination (min 1) (number, optional)
+  - `perPage`: Results per page for pagination (min 1, max 100) (number, optional)
   - `repo`: The name of the repository. (string, required)
   - `resolution`: Filter by resolution (string, optional)
   - `secret_type`: A comma-separated list of secret types to return. All default secret patterns are returned. To return generic patterns, pass the token name(s) in the parameter. (string, optional)
@@ -1485,29 +1492,6 @@ The following sets of tools are available:
 
 </details>
 
-## Dynamic Tool Discovery
-
-**Note**: This feature is currently in beta and is not available in the Remote GitHub MCP Server. Please test it out and let us know if you encounter any issues.
-
-Instead of starting with all tools enabled, you can turn on dynamic toolset discovery. Dynamic toolsets allow the MCP host to list and enable toolsets in response to a user prompt. This should help to avoid situations where the model gets confused by the sheer number of tools available.
-
-### Using Dynamic Tool Discovery
-
-When using the binary, you can pass the `--dynamic-toolsets` flag.
-
-```bash
-./github-mcp-server --dynamic-toolsets
-```
-
-When using Docker, you can pass the toolsets as environment variables:
-
-```bash
-docker run -i --rm \
-  -e GITHUB_PERSONAL_ACCESS_TOKEN=<your-token> \
-  -e GITHUB_DYNAMIC_TOOLSETS=1 \
-  ghcr.io/github/github-mcp-server
-```
-
 ## Read-Only Mode
 
 To run the server in read-only mode, you can use the `--read-only` flag. This will only offer read-only tools, preventing any modifications to repositories, issues, pull requests, etc.

cmd/github-mcp-server/generate_docs.go

@@ -145,8 +145,8 @@ func generateToolsetsDoc(i *inventory.Inventory) string {
 	fmt.Fprintf(&buf, "| %s | `context`               | **Strongly recommended**: Tools that provide context about the current user and GitHub context you are operating in |\n", contextIcon)
 
 	// AvailableToolsets() returns toolsets that have tools, sorted by ID
-	// Exclude context (custom description above) and dynamic (internal only)
-	for _, ts := range i.AvailableToolsets("context", "dynamic") {
+	// Exclude context (custom description above)
+	for _, ts := range i.AvailableToolsets("context") {
 		icon := octiconImg(ts.Icon)
 		fmt.Fprintf(&buf, "| %s | `%s` | %s |\n", icon, ts.ID, ts.Description)
 	}
@@ -346,8 +346,8 @@ func generateRemoteToolsetsDoc() string {
 	fmt.Fprintf(&buf, "| %s<br>`all` | All available GitHub MCP tools | https://api.githubcopilot.com/mcp/ | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=github&config=%%7B%%22type%%22%%3A%%20%%22http%%22%%2C%%22url%%22%%3A%%20%%22https%%3A%%2F%%2Fapi.githubcopilot.com%%2Fmcp%%2F%%22%%7D) | [read-only](https://api.githubcopilot.com/mcp/readonly) | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=github&config=%%7B%%22type%%22%%3A%%20%%22http%%22%%2C%%22url%%22%%3A%%20%%22https%%3A%%2F%%2Fapi.githubcopilot.com%%2Fmcp%%2Freadonly%%22%%7D) |\n", allIcon)
 
 	// AvailableToolsets() returns toolsets that have tools, sorted by ID
-	// Exclude context (handled separately) and dynamic (internal only)
-	for _, ts := range r.AvailableToolsets("context", "dynamic") {
+	// Exclude context (handled separately)
+	for _, ts := range r.AvailableToolsets("context") {
 		idStr := string(ts.ID)
 
 		apiURL := fmt.Sprintf("https://api.githubcopilot.com/mcp/x/%s", idStr)

cmd/github-mcp-server/main.go

@@ -85,7 +85,6 @@ var (
 				EnabledToolsets:      enabledToolsets,
 				EnabledTools:         enabledTools,
 				EnabledFeatures:      enabledFeatures,
-				DynamicToolsets:      viper.GetBool("dynamic_toolsets"),
 				ReadOnly:             viper.GetBool("read-only"),
 				ExportTranslations:   viper.GetBool("export-translations"),
 				EnableCommandLogging: viper.GetBool("enable-command-logging"),
@@ -144,7 +143,6 @@ var (
 				ReadOnly:             viper.GetBool("read-only"),
 				EnabledToolsets:      enabledToolsets,
 				EnabledTools:         enabledTools,
-				DynamicToolsets:      viper.GetBool("dynamic_toolsets"),
 				ExcludeTools:         excludeTools,
 				InsidersMode:         viper.GetBool("insiders"),
 			}
@@ -165,7 +163,6 @@ func init() {
 	rootCmd.PersistentFlags().StringSlice("tools", nil, "Comma-separated list of specific tools to enable")
 	rootCmd.PersistentFlags().StringSlice("exclude-tools", nil, "Comma-separated list of tool names to disable regardless of other settings")
 	rootCmd.PersistentFlags().StringSlice("features", nil, "Comma-separated list of feature flags to enable")
-	rootCmd.PersistentFlags().Bool("dynamic-toolsets", false, "Enable dynamic toolsets")
 	rootCmd.PersistentFlags().Bool("read-only", false, "Restrict the server to read-only operations")
 	rootCmd.PersistentFlags().String("log-file", "", "Path to log file")
 	rootCmd.PersistentFlags().Bool("enable-command-logging", false, "When enabled, the server will log all command requests and responses to the log file")
@@ -187,7 +184,6 @@ func init() {
 	_ = viper.BindPFlag("tools", rootCmd.PersistentFlags().Lookup("tools"))
 	_ = viper.BindPFlag("exclude_tools", rootCmd.PersistentFlags().Lookup("exclude-tools"))
 	_ = viper.BindPFlag("features", rootCmd.PersistentFlags().Lookup("features"))
-	_ = viper.BindPFlag("dynamic_toolsets", rootCmd.PersistentFlags().Lookup("dynamic-toolsets"))
 	_ = viper.BindPFlag("read-only", rootCmd.PersistentFlags().Lookup("read-only"))
 	_ = viper.BindPFlag("log-file", rootCmd.PersistentFlags().Lookup("log-file"))
 	_ = viper.BindPFlag("enable-command-logging", rootCmd.PersistentFlags().Lookup("enable-command-logging"))

docs/installation-guides/README.md

@@ -104,6 +104,5 @@ If you encounter issues:
 After installation, you may want to explore:
 - **Toolsets**: Enable/disable specific GitHub API capabilities
 - **Read-Only Mode**: Restrict to read-only operations
-- **Dynamic Tool Discovery**: Enable tools on-demand
 - **Lockdown Mode**: Hide public issue details created by users without push access
 

docs/server-configuration.md

@@ -11,7 +11,6 @@ We currently support the following ways in which the GitHub MCP Server can be co
 | Individual Tools | `X-MCP-Tools` header | `--tools` flag or `GITHUB_TOOLS` env var |
 | Exclude Tools | `X-MCP-Exclude-Tools` header | `--exclude-tools` flag or `GITHUB_EXCLUDE_TOOLS` env var |
 | Read-Only Mode | `X-MCP-Readonly` header or `/readonly` URL | `--read-only` flag or `GITHUB_READ_ONLY` env var |
-| Dynamic Mode | Not available | `--dynamic-toolsets` flag or `GITHUB_DYNAMIC_TOOLSETS` env var |
 | Lockdown Mode | `X-MCP-Lockdown` header | `--lockdown-mode` flag or `GITHUB_LOCKDOWN_MODE` env var |
 | Insiders Mode | `X-MCP-Insiders` header or `/insiders` URL | `--insiders` flag or `GITHUB_INSIDERS` env var |
 | Feature Flags | `X-MCP-Features` header | `--features` flag |
@@ -24,7 +23,7 @@ We currently support the following ways in which the GitHub MCP Server can be co
 
 ## How Configuration Works
 
-All configuration options are **composable**: you can combine toolsets, individual tools, excluded tools, dynamic discovery, read-only mode and lockdown mode in any way that suits your workflow.
+All configuration options are **composable**: you can combine toolsets, individual tools, excluded tools, read-only mode and lockdown mode in any way that suits your workflow.
 
 Note: **read-only** mode acts as a strict security filter that takes precedence over any other configuration, by disabling write tools even when explicitly requested.
 
@@ -287,59 +286,6 @@ When active, this mode will disable all tools that are not read-only even if the
 
 ---
 
-### Dynamic Discovery (Local Only)
-
-**Best for:** Letting the LLM discover and enable toolsets as needed.
-
-Starts with only discovery tools (`enable_toolset`, `list_available_toolsets`, `get_toolset_tools`), then expands on demand.
-
-<table>
-<tr><th>Local Server Only</th></tr>
-<tr valign="top">
-<td>
-
-```json
-{
-  "type": "stdio",
-  "command": "go",
-  "args": [
-    "run",
-    "./cmd/github-mcp-server",
-    "stdio",
-    "--dynamic-toolsets"
-  ],
-  "env": {
-    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
-  }
-}
-```
-
-**With some tools pre-enabled:**
-```json
-{
-  "type": "stdio",
-  "command": "go",
-  "args": [
-    "run",
-    "./cmd/github-mcp-server",
-    "stdio",
-    "--dynamic-toolsets",
-    "--tools=get_me,search_code"
-  ],
-  "env": {
-    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
-  }
-}
-```
-
-</td>
-</tr>
-</table>
-
-When both dynamic mode and specific tools are enabled in the server configuration, the server will start with the 3 dynamic tools + the specified tools.
-
----
-
 ### Lockdown Mode
 
 **Best for:** Public repositories where you want to limit content from users without push access.
@@ -521,7 +467,6 @@ See [Scope Filtering](./scope-filtering.md) for details on how filtering works w
 | Server fails to start | Invalid tool name in `--tools` or `X-MCP-Tools` | Check tool name spelling; use exact names from [Tools list](../README.md#tools) |
 | Write tools not working | Read-only mode enabled | Remove `--read-only` flag or `X-MCP-Readonly` header |
 | Tools missing | Toolset not enabled | Add the required toolset or specific tool |
-| Dynamic tools not available | Using remote server | Dynamic mode is available in the local MCP server only |
 
 ---
 

docs/toolsets-and-icons.md

@@ -161,7 +161,6 @@ icons := octicons.Icons("repo")
 | Labels | `tag` |
 | Stargazers | `star` |
 | Notifications | `bell` |
-| Dynamic | `tools` |
 | Copilot | `copilot` |
 | Support Search | `book` |