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Bump dependencies and enhance GitHub Actions toolset functionality#1

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Bump dependencies and enhance GitHub Actions toolset functionality#1
WyattCrypto88 wants to merge 601 commits into
gh-repo-clone-WyattCrypto88/github-mcp-serverfrom
main

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Summary

Why

Fixes #

What changed

MCP impact

  • No tool or API changes
  • Tool schema or behavior changed
  • New tool added

Prompts tested (tool changes only)

Security / limits

  • No security or limits impact
  • Auth / permissions considered
  • Data exposure, filtering, or token/size limits considered

Tool renaming

  • I am renaming tools as part of this PR (e.g. a part of a consolidation effort)
    • I have added the new tool aliases in deprecated_tool_aliases.go
  • I am not renaming tools as part of this PR

Note: if you're renaming tools, you must add the tool aliases. For more information on how to do so, please refer to the official docs.

Lint & tests

  • Linted locally with ./script/lint
  • Tested locally with ./script/test

Docs

  • Not needed
  • Updated (README / docs / examples)

mattdholloway and others added 30 commits January 5, 2026 10:14
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Fallback to default branch in get_file_contents when main doesn't exist

* Addressing review comments

* Improvements to push_files tool

* Fixed copilot comments

* Addressing review comments

* Remove debug statement
- Created pkg/scopes package with OAuth scope constants
- Added RequiredScopes and AcceptedScopes fields to ServerTool
- Added NewToolWithScopes helpers in dependencies.go
- Updated context tools (get_me, get_teams, get_team_members) with scopes

Co-authored-by: SamMorrowDrums <4811358+SamMorrowDrums@users.noreply.github.com>
- Updated 60+ tools with required and accepted OAuth scopes
- Added scopes to: gists, git, notifications, projects, code scanning,
  dependabot, secret scanning, security advisories, actions, discussions,
  issues (partial), labels, pull requests (partial), repositories (partial), search (partial)
- Remaining: ~20 tools in issues, pullrequests, repositories, and search files

Co-authored-by: SamMorrowDrums <4811358+SamMorrowDrums@users.noreply.github.com>
- Updated all remaining tools with OAuth scope information
- Added scope documentation generation to generate-docs command
- Documentation now shows Required and Accepted OAuth scopes for each tool
- All 100+ tools now have scope information defined
- Tests pass, linter passes, documentation generated successfully

Co-authored-by: SamMorrowDrums <4811358+SamMorrowDrums@users.noreply.github.com>
- Replace NewToolWithScopes with updated NewTool that includes scope parameters
- All tools now use the same constructor with explicit scope requirements
- Documentation only shows accepted scopes when they differ from required
- Removed NewToolWithScopes and NewToolFromHandlerWithScopes helper functions

Co-authored-by: SamMorrowDrums <4811358+SamMorrowDrums@users.noreply.github.com>
- Add ScopeHierarchy map defining parent-child scope relationships
- Add ExpandScopes() function to derive accepted scopes from required scopes
- Update NewTool/NewToolFromHandler to take []scopes.Scope and auto-derive AcceptedScopes
- Add new scope constants: NoScope, User, ReadUser, UserEmail, ReadPackages, WritePackages
- Update all tool files to use new signature with typed scopes
- Add comprehensive tests for ExpandScopes

The scope hierarchy allows automatic derivation of accepted scopes:
- repo → public_repo, security_events
- admin:org → write:org → read:org
- project → read:project
- write:packages → read:packages
- user → read:user, user:email

This enables the remote server to consume scope info directly from OSS tools.
public_repo is implicit - the GitHub API handles the distinction between
public and private repos. Using repo as the required scope is more
consistent with our enforcement model:
- PATs: tools visible if token has repo scope
- OAuth: scope challenge requests repo scope
Map iteration in Go is non-deterministic, which causes doc generation
to produce different output on each run. Sort the scope slices in:
- ScopeSet.ToSlice()
- ScopeSet.ToStringSlice()
- ExpandScopes()
Add the ability to filter tools based on token scopes for PAT users.
This uses an HTTP HEAD request to GitHub's API to discover token scopes.

New components:
- pkg/scopes/filter.go: HasRequiredScopes checks if scopes satisfy tool requirements
- pkg/scopes/fetcher.go: FetchTokenScopes gets scopes via HTTP HEAD to GitHub API
- pkg/github/scope_filter.go: CreateScopeFilter creates inventory.ToolFilter

Integration:
- Add --filter-by-scope flag to stdio command (disabled by default)
- When enabled, fetches token scopes on startup
- Tools requiring unavailable scopes are hidden from tool list
- Gracefully continues without filtering if scope fetch fails (logs warning)

This allows the OSS server to have similar scope-based tool visibility
as the remote server, and the filter logic can be reused by remote server.
Scope filtering is now a built-in feature rather than a configurable option.
The server automatically fetches token scopes at startup and filters tools
accordingly. If scope detection fails, it logs a warning and continues with
all tools available.
- Scope filtering only applies to classic PATs which return X-OAuth-Scopes
- Fine-grained PATs and other token types skip filtering (all tools shown)
- Updated docs to clarify PAT filtering vs OAuth scope challenges
The README already has auto-generated tool documentation with scopes.
Keep only the scope hierarchy explanation which is structural.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…cts tests (github#1737)

* Initial plan

* migrate tests from go-github-mock to internal testify-based mock

Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>

* address feedback in testmock helper

Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>

* tweak testmock path matching edge case

Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>

* refine testmock options and path matching

Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>

* simplify matchPath and document delete endpoint

Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>

* Replace go-github-mock usage in tests with shared HTTP mock helper

Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>

* Replace go-github-mock usage in tests with shared HTTP mock helper

Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>

* fix tests and lint after mock cleanup

Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>

* Remove import completely

* Partial removal in repositories_test.go

* Final removal

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: JoannaaKL <67866556+JoannaaKL@users.noreply.github.com>
Co-authored-by: JoannaaKL <joannaakl@github.com>
mattdholloway and others added 30 commits April 15, 2026 17:36
Upgrade the MCP Go SDK from v1.3.1-0.20260220105450-b17143f71798
(pseudo-version) to v1.5.0 (latest stable).

This also resolves github#2333, as the SDK now correctly handles
Content-Type headers with MIME parameters (e.g. charset=utf-8)
via mime.ParseMediaType in StreamableHTTPHandler (added in v1.4.1).

Transitive dependency updates:
- go directive: 1.24.0 → 1.25.0 (required by SDK)
- golang.org/x/oauth2: v0.34.0 → v0.35.0
- golang.org/x/sys: v0.40.0 → v0.41.0
- segmentio/encoding: v0.5.3 → v0.5.4

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Auto-generated by license-check workflow
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Bumps [docker/login-action](https://github.com/docker/login-action) from 3.7.0 to 4.0.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](docker/login-action@c94ce9f...b45d80f)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-version: 4.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
The README references docs/deprecated-tool-aliases.md which does not
exist. The correct file is docs/tool-renaming.md.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.12.0 to 4.0.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](docker/setup-buildx-action@8d2750c...4d04d5d)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-version: 4.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [github.com/josephburnett/jd/v2](https://github.com/josephburnett/jd) from 2.4.0 to 2.5.0.
- [Release notes](https://github.com/josephburnett/jd/releases)
- [Changelog](https://github.com/josephburnett/jd/blob/master/RELEASE_NOTES.md)
- [Commits](josephburnett/jd@v2.4.0...v2.5.0)

---
updated-dependencies:
- dependency-name: github.com/josephburnett/jd/v2
  dependency-version: 2.5.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Auto-generated by license-check workflow
Bumps golang from 1.25.8-alpine to 1.25.9-alpine.

---
updated-dependencies:
- dependency-name: golang
  dependency-version: 1.25.9-alpine
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Rebase PR github#2282 onto main (post-github#2332) and unify feature flag
allowlists into a single source of truth.

- Add MCPAppsFeatureFlag, AllowedFeatureFlags, InsidersFeatureFlags,
  and ResolveFeatureFlags in feature_flags.go
- AllowedFeatureFlags includes all user-controllable flags (MCP Apps +
  granular), InsidersFeatureFlags only includes MCPAppsFeatureFlag
- HeaderAllowedFeatureFlags() now delegates to AllowedFeatureFlags
- Builder uses feature checker instead of insidersMode bool
- Remove InsidersOnly field from ServerTool and WithInsidersMode from
  Builder
- HTTP feature checker uses ResolveFeatureFlags for per-request
  resolution with insiders expansion
- Tool handlers check MCPAppsFeatureFlag via IsFeatureEnabled instead
  of InsidersMode

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
)

* Initial plan

* Enforce exactly one value key per field in set_issue_fields and add tests

Address review feedback:
- Change validation to count value keys and reject when multiple are
  provided (e.g., text_value + number_value, or text_value + delete).
- Add unit tests for multiple value keys and value + delete scenarios.
- Run generate-docs (no doc changes needed; README was already current).

Agent-Logs-Url: https://github.com/github/github-mcp-server/sessions/7e89edb3-5315-42dd-bfa1-6c962f1ba137

Co-authored-by: mattdholloway <918573+mattdholloway@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: mattdholloway <918573+mattdholloway@users.noreply.github.com>
Add NormalizeContentType middleware that strips optional parameters
(e.g. charset=utf-8) from application/json Content-Type headers before
the request reaches the Go SDK's StreamableHTTP handler, which performs
strict string matching.

Per RFC 8259, the charset parameter is redundant for JSON but must be
accepted per HTTP semantics.

Fixes github#2333

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Upgrades github.com/modelcontextprotocol/go-sdk from v1.5.0 to
v1.5.1-0.20260403154220-27f29c1cef3b which includes proper media type
parsing for Content-Type headers, fixing the strict string matching
that rejected application/json; charset=utf-8.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
The go-sdk bump (27f29c1) includes the proper fix upstream, making
the middleware unnecessary.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Auto-generated by license-check workflow
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Agent-Logs-Url: https://github.com/github/github-mcp-server/sessions/49811f97-33b0-476c-8811-419dee2a5318

Co-authored-by: omgitsads <4619+omgitsads@users.noreply.github.com>
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 7.0.0 to 7.1.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](docker/build-push-action@d08e5c3...bcafcac)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-version: 7.1.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/github-script](https://github.com/actions/github-script) from 8 to 9.
- [Release notes](https://github.com/actions/github-script/releases)
- [Commits](actions/github-script@v8...v9)

---
updated-dependencies:
- dependency-name: actions/github-script
  dependency-version: '9'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps golang from `04d017a` to `5caaf1c`.

---
updated-dependencies:
- dependency-name: golang
  dependency-version: 1.25.9-alpine
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
…FieldValue union (github#2366)

* Fix set_issue_fields mutation: use correct inline fragments for IssueFieldValue union

The mutation response struct used a single inline fragment
'... on IssueFieldDateValue' with a 'Name' field that doesn't exist
on that type (only IssueFieldSingleSelectValue has 'name'). This
caused GraphQL validation to fail with:

  Field 'name' doesn't exist on type 'IssueFieldDateValue'

Since GraphQL validates the entire document (including response
selection sets) before executing any operation, the mutation never
fired at all — no fields were ever set regardless of input.

Fix by adding correct inline fragments for all four union types:
- IssueFieldTextValue (value)
- IssueFieldSingleSelectValue (name)
- IssueFieldDateValue (value)
- IssueFieldNumberValue (value)

* Update test mock to match corrected inline fragments

* Update handler_test.go formatting
* use REST API for permission checks

* update tests

* skip API call for bots and add github-action[bot] to trusted logins

* improve tests

* add nil guard to IsSafeContent

* add comment clarifying maintain mapping

---------

Co-authored-by: Sam Morrow <info@sam-morrow.com>
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