- Extract ServerTool struct into pkg/toolsets/server_tool.go
- Add ToolDependencies struct for passing common dependencies to handlers
- HandlerFunc allows lazy handler generation from Tool definitions
- NewServerTool for new dependency-based tools
- NewServerToolLegacy for backward compatibility with existing handlers
- Update toolsets.go to store and pass dependencies
- Update all call sites to use NewServerToolLegacy

Co-authored-by: Adam Holt <4619+omgitsads@users.noreply.github.com>

- Move ToolDependencies to pkg/github/dependencies.go with proper types
- Use 'any' in toolsets package to avoid circular dependencies
- Add NewTool/NewToolFromHandler helpers that isolate type assertion
- Tool implementations will be fully typed with no assertions scattered
- Infrastructure ready for incremental tool migration

Migrate search.go tools (SearchRepositories, SearchCode, SearchUsers,
SearchOrgs) to use the new NewTool helper and ToolDependencies pattern.

- Functions now take only TranslationHelperFunc and return ServerTool
- Handler generation uses ToolDependencies for typed access to clients
- Update tools.go call sites to remove getClient parameter
- Update tests to use new Handler(deps) pattern

This demonstrates the migration pattern for additional tool files.

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* Add repos toolset instructions

* 1. Make sha optional (if not supplied - GetContents is used to retrieve original sha)
2. Instruct LLM to supply actual sha using git command and move instructions to tool description.

* Update toolsnaps and docs

* Better error handling

* Add tests

* Clearing resources in time

* Addressing review comments && checking etag

* Test fixes

* docs: add Antigravity installation guide

* docs: improve antigravity guide and address feedback

* Update docs/installation-guides/install-antigravity.md

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update docs/installation-guides/install-antigravity.md

Co-authored-by: Iryna Kulakova <52420926+IrynaKulakova@users.noreply.github.com>

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Iryna Kulakova <52420926+IrynaKulakova@users.noreply.github.com>

* update docs

* Update docs/tool-renaming.md

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* refactor(search): migrate search tools to new ServerTool pattern

Migrate search.go tools (SearchRepositories, SearchCode, SearchUsers,
SearchOrgs) to use the new NewTool helper and ToolDependencies pattern.

- Functions now take only TranslationHelperFunc and return ServerTool
- Handler generation uses ToolDependencies for typed access to clients
- Update tools.go call sites to remove getClient parameter
- Update tests to use new Handler(deps) pattern

This demonstrates the migration pattern for additional tool files.

Co-authored-by: Adam Holt <oholt@github.com>

* Migrate context_tools to new ServerTool pattern

Convert GetMe, GetTeams, and GetTeamMembers to use the new typed
dependency injection pattern:
- Functions now take only translations helper, return toolsets.ServerTool
- Handler is generated lazily via deps.GetClient/deps.GetGQLClient
- Tests updated to use serverTool.Handler(deps) pattern
- Fixed error return pattern to return nil for Go error (via result.IsError)

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* refactor(gists): migrate gists.go to NewTool pattern (#1591)

* Migrate context_tools to new ServerTool pattern

Convert GetMe, GetTeams, and GetTeamMembers to use the new typed
dependency injection pattern:
- Functions now take only translations helper, return toolsets.ServerTool
- Handler is generated lazily via deps.GetClient/deps.GetGQLClient
- Tests updated to use serverTool.Handler(deps) pattern
- Fixed error return pattern to return nil for Go error (via result.IsError)

Co-authored-by: Adam Holt <oholt@github.com>

* refactor(gists): migrate gists.go to NewTool pattern

Convert all gist tools (ListGists, GetGist, CreateGist, UpdateGist)
to use the new NewTool helper with ToolDependencies injection.

- Remove getClient parameter from function signatures
- Use deps.GetClient(ctx) inside handlers
- Standardize error handling with utils.NewToolResultErrorFromErr()
- Update all tests to use serverTool.Handler(deps) pattern

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

---------

Co-authored-by: Adam Holt <oholt@github.com>
Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

---------

Co-authored-by: Adam Holt <oholt@github.com>
Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

…1592)

* refactor(notifications): migrate notifications.go to NewTool pattern

Convert all notification tools to use the new NewTool helper with
ToolDependencies injection.

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* Refactor repositories.go tools to use NewTool pattern with ToolDependencies

Convert all 18 tool functions in repositories.go to use the new NewTool helper
pattern with typed ToolDependencies, isolating type assertions to a single
location and improving code maintainability.

Functions converted:
- GetCommit, ListCommits, ListBranches
- CreateOrUpdateFile, CreateRepository, GetFileContents
- ForkRepository, DeleteFile, CreateBranch, PushFiles
- ListTags, GetTag, ListReleases, GetLatestRelease, GetReleaseByTag
- ListStarredRepositories, StarRepository, UnstarRepository

This is part of a stacked PR series to systematically migrate all tool
files to the new pattern.

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* refactor(issues): migrate issues.go to NewTool pattern

Convert all 8 tool functions in issues.go to use the new NewTool
helper pattern which standardizes dependency injection:

- IssueRead: GetClient, GetGQLClient, RepoAccessCache, Flags
- ListIssueTypes: GetClient
- AddIssueComment: GetClient
- SubIssueWrite: GetClient
- SearchIssues: GetClient
- IssueWrite: GetClient, GetGQLClient
- ListIssues: GetGQLClient
- AssignCopilotToIssue: GetGQLClient

Updated tools.go to use direct function calls instead of
NewServerToolLegacy wrappers. Updated all tests in issues_test.go
to use the new ToolDependencies pattern and Handler() method.

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* refactor(pullrequests): convert PR tools to NewTool pattern

Convert all 10 pull request tool functions to use the NewTool
pattern with ToolDependencies injection:
- PullRequestRead
- CreatePullRequest
- UpdatePullRequest
- ListPullRequests
- MergePullRequest
- SearchPullRequests
- UpdatePullRequestBranch
- PullRequestReviewWrite
- AddCommentToPendingReview
- RequestCopilotReview

Update tools.go to use direct function calls (removing
NewServerToolLegacy wrappers) for PR functions.

Update all tests in pullrequests_test.go to use the new
handler pattern with deps and 2-value return.

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* Refactor actions.go to use NewTool pattern

Convert all 14 tool functions in actions.go to use the NewTool pattern with
ToolDependencies for dependency injection. This is part of a broader effort
to standardize the tool implementation pattern across the codebase.

Changes:
- ListWorkflows, ListWorkflowRuns, RunWorkflow, GetWorkflowRun
- GetWorkflowRunLogs, ListWorkflowJobs, GetJobLogs
- RerunWorkflowRun, RerunFailedJobs, CancelWorkflowRun
- ListWorkflowRunArtifacts, DownloadWorkflowRunArtifact
- DeleteWorkflowRunLogs, GetWorkflowRunUsage

The new pattern:
- Takes only translations.TranslationHelperFunc as parameter
- Returns toolsets.ServerTool with Tool and Handler
- Handler receives ToolDependencies for client access
- Enables better testability and consistent interface

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* refactor(git): migrate GetRepositoryTree to NewTool pattern

* refactor(security): migrate code_scanning, secret_scanning, dependabot to NewTool pattern

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* refactor(discussions): migrate to NewTool pattern

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* Refactor security_advisories tools to use NewTool pattern

Convert 4 functions from NewServerToolLegacy wrapper to NewTool:
- ListGlobalSecurityAdvisories
- GetGlobalSecurityAdvisory
- ListRepositorySecurityAdvisories
- ListOrgRepositorySecurityAdvisories

Update tools.go toolset registration and tests.

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* refactor: convert projects, labels, and dynamic_tools to NewTool pattern

This PR converts projects.go, labels.go, and dynamic_tools.go from the
legacy NewServerToolLegacy wrapper pattern to the new NewTool pattern with
proper ToolDependencies.

Changes:
- projects.go: Convert all 9 project functions to use NewTool with
  ToolHandlerFor[map[string]any, any] and 3-return-value handlers
- projects_test.go: Update tests to use new serverTool.Handler(deps) pattern
- labels.go: Convert GetLabel, ListLabels, and LabelWrite to NewTool pattern
- labels_test.go: Update tests to use new pattern
- dynamic_tools.go: Refactor functions to return ServerTool directly
  (using NewServerToolLegacy internally since they have special dependencies)
- tools.go: Remove NewServerToolLegacy wrappers for dynamic tools registration

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>

* Add --features CLI flag for feature flag support

Add CLI flag and config support for feature flags in the local server:

- Add --features flag to main.go (StringSlice, comma-separated)
- Add EnabledFeatures field to StdioServerConfig and MCPServerConfig
- Create createFeatureChecker() that builds a set from enabled features
- Wire WithFeatureChecker() into the toolset group filter chain

This enables tools/resources/prompts that have FeatureFlagEnable set to
a flag name that is passed via --features. The checker uses a simple
set membership test for O(1) lookup.

Usage:
  github-mcp-server stdio --features=my_feature,another_feature
  GITHUB_FEATURES=my_feature github-mcp-server stdio

* Add validation tests for tools, resources, and prompts metadata

This commit adds comprehensive validation tests to ensure all MCP items
have required metadata:

- TestAllToolsHaveRequiredMetadata: Validates Toolset.ID and Annotations
- TestAllToolsHaveValidToolsetID: Ensures toolsets are in AvailableToolsets()
- TestAllResourcesHaveRequiredMetadata: Validates resource metadata
- TestAllPromptsHaveRequiredMetadata: Validates prompt metadata
- TestToolReadOnlyHintConsistency: Validates IsReadOnly() matches annotation
- TestNoDuplicate*Names: Ensures unique names across tools/resources/prompts
- TestAllToolsHaveHandlerFunc: Ensures all tools have handlers
- TestDefaultToolsetsAreValid: Validates default toolset IDs
- TestToolsetMetadataConsistency: Ensures consistent descriptions per toolset

Also fixes a bug discovered by these tests: ToolsetMetadataGit was defined
but not added to AvailableToolsets(), causing get_repository_tree to have
an invalid toolset ID.

* Fix default toolsets behavior when not in dynamic mode

When no toolsets are specified and dynamic mode is disabled, the server
should use the default toolsets. The bug was introduced when adding
dynamic toolsets support:

1. CleanToolsets(nil) was converting nil to empty slice
2. Empty slice passed to WithToolsets means 'no toolsets'
3. This resulted in zero tools being registered

Fix: Preserve nil for non-dynamic mode (nil = use defaults in WithToolsets)
and only set empty slice when dynamic mode is enabled without explicit
toolsets.

* refactor: address PR review feedback for toolsets

- Rename AddDeprecatedToolAliases to WithDeprecatedToolAliases for
  immutable filter chain consistency (returns new ToolsetGroup)
- Remove unused mockGetRawClient from generate_docs.go (use nil instead)
- Remove legacy ServerTool functions (NewServerToolLegacy and
  NewServerToolFromHandlerLegacy) - no usages
- Add panic in Handler()/RegisterFunc() when HandlerFunc is nil
- Add HasHandler() method for checking if tool has a handler
- Add tests for HasHandler and nil handler panic behavior
- Update all tests to use new WithDeprecatedToolAliases pattern

* refactor: Apply HandlerFunc pattern to resources for stateless NewToolsetGroup

This change applies the same HandlerFunc pattern used by tools to resources,
allowing NewToolsetGroup to be fully stateless (only requiring translations).

Key changes:
- Add ResourceHandlerFunc type to toolsets package
- Update ServerResourceTemplate to use HandlerFunc instead of direct Handler
- Add HasHandler() and Handler(deps) methods to ServerResourceTemplate
- Update RegisterResourceTemplates to take deps parameter
- Refactor repository resource definitions to use HandlerFunc pattern
- Make AllResources(t) stateless (only takes translations)
- Make NewToolsetGroup(t) stateless (only takes translations)
- Update generate_docs.go - no longer needs mock clients
- Update tests to use new patterns

This resolves the concern about mixed concerns in doc generation - the
toolset metadata and resource templates can now be created without any
runtime dependencies, while handlers are generated on-demand when deps
are provided during registration.

* refactor: simplify ForMCPRequest switch cases

* refactor(generate_docs): use strings.Builder and AllTools() iteration

- Replace slice joining with strings.Builder for all doc generation
- Iterate AllTools() directly instead of ToolsetIDs()/ToolsForToolset()
- Removes need for special 'dynamic' toolset handling (no tools = no output)
- Context toolset still explicitly handled for custom description
- Consistent pattern across generateToolsetsDoc, generateToolsDoc,
  generateRemoteToolsetsDoc, and generateDeprecatedAliasesTable

* feat(toolsets): add AvailableToolsets() with exclude filter

- Add AvailableToolsets() method that returns toolsets with actual tools
- Support variadic exclude parameter for filtering out specific toolsets
- Simplifies doc generation by removing manual skip logic
- Naturally excludes empty toolsets (like 'dynamic') without special cases

* refactor(generate_docs): hoist success logging to generateAllDocs

* refactor: consolidate toolset validation into ToolsetGroup

- Add Default field to ToolsetMetadata and derive defaults from metadata
- Move toolset validation into WithToolsets (trims whitespace, dedupes, tracks unrecognized)
- Add UnrecognizedToolsets() method for warning about typos
- Add DefaultToolsetIDs() method to derive defaults from metadata
- Remove redundant functions: CleanToolsets, GetValidToolsetIDs, AvailableToolsets, GetDefaultToolsetIDs
- Update DynamicTools to take ToolsetGroup for schema enum generation
- Add stubTranslator for cases needing ToolsetGroup without translations

This eliminates hardcoded toolset lists - everything is now derived from
the actual registered tools and their metadata.

* refactor: rename toolsets package to registry with builder pattern

- Rename pkg/toolsets to pkg/registry (better reflects its purpose)
- Split monolithic toolsets.go into focused files:
  - registry.go: Core Registry struct and MCP methods
  - builder.go: Builder pattern for creating Registry instances
  - filters.go: All filtering logic (toolsets, read-only, feature flags)
  - resources.go: ServerResourceTemplate type
  - prompts.go: ServerPrompt type
  - errors.go: Error types
  - server_tool.go: ServerTool and ToolsetMetadata (existing)
- Fix lint: Rename RegistryBuilder to Builder (avoid stuttering)
- Update all imports across ~45 files

This refactoring improves code organization and makes the registry's
purpose clearer. The builder pattern provides a clean API:

  reg := registry.NewBuilder().
      SetTools(tools).
      WithReadOnly(true).
      WithToolsets([]string{"repos"}).
      Build()

* fix: remove unnecessary type arguments in helper_test.go

* fix: restore correct behavior for --tools and --toolsets flags

Two behavioral regressions were fixed in resolveEnabledToolsets():

1. When --tools=X is used without --toolsets, the server should only
   register the specified tools, not the default toolsets. Now returns
   an empty slice instead of nil when EnabledTools is set.

2. When --toolsets=all --dynamic-toolsets is used, the 'all' and 'default'
   pseudo-toolsets should be removed so only the dynamic management tools
   are registered. This matches the original pre-refactor behavior.

* Move labels tools to issues toolset

Labels are closely related to issues - you add labels to issues,
search issues by label, etc. Keeping them in a separate toolset
required users to explicitly enable 'labels' to get this functionality.

Moving to issues toolset makes labels available by default since
issues is a default toolset.

* Restore labels toolset with get_label in both issues and labels

This restores conformance with the original behavior where:
- get_label is in issues toolset (read-only label access for issue workflows)
- get_label, list_label, label_write are in labels toolset (full management)

The duplicate get_label registration is intentional - it was in both toolsets
in the original implementation. Added test exception to allow this case.

* Fix instruction generation and capability advertisement

- Expand nil toolsets to default IDs before GenerateInstructions
  (nil means 'use defaults' in registry but instructions need actual names)
- Remove unconditional HasTools/HasResources/HasPrompts=true in NewServer
  (let SDK determine capabilities based on registered items, matching main)

* Add tests for dynamic toolset management tools

Tests cover:
- list_available_toolsets: verifies toolsets are listed with enabled status
- get_toolset_tools: verifies tools can be retrieved for a toolset
- enable_toolset: verifies toolset can be enabled and marked as enabled
- enable_toolset invalid: verifies proper error for non-existent toolset
- toolsets enum: verifies tools have proper enum values in schema

* Advertise all capabilities in dynamic toolsets mode

In dynamic mode, explicitly set HasTools/HasResources/HasPrompts=true
since toolsets with those capabilities can be enabled at runtime.
This ensures clients know the server supports these features even
when no tools/resources/prompts are initially registered.

* Improve conformance test with dynamic tool calls and JSON normalization

- Add dynamic tool call testing (list_available_toolsets, get_toolset_tools, enable_toolset)
- Parse and sort embedded JSON in text fields for proper comparison
- Separate progress output (stderr) from summary (stdout) for CI
- Add test type field to distinguish standard vs dynamic tests

* Add conformance-report to .gitignore

* Add conformance test CI workflow

- Runs on pull requests to main
- Compares PR branch against merge-base with origin/main
- Outputs full conformance report to GitHub Actions Job Summary
- Uploads detailed report as artifact for deeper investigation
- Does not fail the build on differences (may be intentional)

* Add map indexes for O(1) lookups in Registry

Address review feedback to use maps for collections. Added lookup maps
(toolsByName, resourcesByURI, promptsByName) while keeping slices for
ordered iteration. This provides O(1) lookup for:

- FindToolByName
- filterToolsByName (used by ForMCPRequest)
- filterResourcesByURI
- filterPromptsByName

Maps are built once during Build() and shared in ForMCPRequest copies.

* perf(registry): O(1) HasToolset lookup via pre-computed set

Add toolsetIDSet (map[ToolsetID]bool) to Registry for O(1) HasToolset lookups.
Previously HasToolset iterated through all tools, resourceTemplates, and prompts
to check if any belonged to the given toolset. Now it's a simple map lookup.

The set is populated during the single-pass processToolsets() call, which already
collected all valid toolset IDs. This adds zero new iteration - just returns the
existing validIDs map.

processToolsets now returns 6 values:
- enabledToolsets, unrecognized, toolsetIDs, toolsetIDSet, defaultToolsetIDs, descriptions

* simplify: remove lazy toolsByName map - not needed for actual use cases

FindToolByName() is only called once per request at most (to find toolset ID
for dynamic enablement). The SDK handles tool dispatch after registration.

A simple linear scan over ~90 tools is trivially fast and avoids:
- sync.Once complexity
- Map allocation
- Premature optimization for non-existent 'repeated lookups'

The pre-computed maps we keep (toolsetIDSet, etc.) are justified because
they're used for filtering logic that runs on every request.

* Add generic tool filtering mechanisms to registry package

- Add Enabled field to ServerTool for self-filtering based on context
- Add ToolFilter type and WithFilter method to Builder for cross-cutting filters
- Update isToolEnabled to check Enabled function and builder filters in order:
  1. Tool's Enabled function
  2. Feature flags (FeatureFlagEnable/FeatureFlagDisable)
  3. Read-only filter
  4. Builder filters
  5. Toolset/additional tools check
- Add FilteredTools method to Registry as alias for AvailableTools
- Add comprehensive tests for all new functionality
- All tests pass and linter is clean

Closes #1618

Co-authored-by: SamMorrowDrums <4811358+SamMorrowDrums@users.noreply.github.com>

* docs: improve filter evaluation order and FilteredTools documentation

- Add numbered filter evaluation order to isToolEnabled function doc
- Number inline comments for each filter step (1-5)
- Clarify FilteredTools error return is for future extensibility
- Document that library consumers may need to surface recoverable errors

Addresses review feedback on PR #1620

* Refactor GenerateToolsetsHelp() to use strings.Builder pattern

Co-authored-by: SamMorrowDrums <4811358+SamMorrowDrums@users.noreply.github.com>

---------

Co-authored-by: Adam Holt <omgitsads@users.noreply.github.com>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: SamMorrowDrums <4811358+SamMorrowDrums@users.noreply.github.com>

Preserves registry pattern architecture while incorporating:
- Antigravity installation guide
- Tool renaming documentation
- CONTRIBUTING.md updates
- README tool documentation updates

Functional changes from main (5a4338c, a48e306, afe34d8) to be ported separately.

Port three functional improvements from main branch:
- GraphQL review comments grouped as threads (#1554)
- get_file_contents description improvement (#1582)
- create_or_update_file SHA validation fix (#1621)

Adapted implementations to use the new registry pattern with:
- BaseDeps for providing clients via ToolDependencies interface
- deps.GetClient(ctx) and deps.GetGQLClient(ctx) patterns
- Updated tests to use GraphQL mocks for review comments
- Added SHA validation test cases for create_or_update_file

- Fix DefaultToolsetIDs() type mismatch by using github.GetDefaultToolsetIDs()
- Add waitForRateLimit() to check and wait for rate limits before each test
- Add skip conditions for Copilot tests when Copilot isn't available
- Use multi-line file content in TestPullRequestReviewCommentSubmit for
  multi-line review comments to work correctly
- Improve error messages to include response details

The gists.go file was using NewToolResultErrorFromErr for GitHub API
errors, which breaks the error middleware tracking that the remote
server uses for observability and incident detection.

Changed API errors (client.Gists.List, Get, Create, Edit) to use
ghErrors.NewGitHubAPIErrorResponse which properly:
- Records errors in the context for middleware access
- Preserves the response object for rate limit and status tracking
- Maintains consistency with other tools that use this pattern

This ensures production observability is maintained for Gist operations.