Reimplement issue dependencies on go-github v89 REST API

Issue dependencies (blocked_by / blocking) were implemented on GraphQL via
githubv4. Because the pinned githubv4 library predates the dependency
mutations, the code hand-declared AddBlockedByInput / RemoveBlockedByInput
and resolved issue numbers to node IDs with a custom aliased query.

go-github v89 adds first-class REST methods (ListBlockedBy, ListBlocking,
AddBlockedBy, RemoveBlockedBy), so switch issue_dependency_read and
issue_dependency_write to those. This removes the workaround, aligns the
tools with the rest of the REST-based issue tooling, and simplifies tests.

- Bump go-github v87 -> v89 across the module.
- Adapt gists.go to v89: Gists.Create takes CreateGistRequest by value and
  Gists.Edit is renamed to Gists.Update with UpdateGistRequest.
- Update repositories_test.go for RepositoryRelease value-type fields.
- Rewrite issue_dependencies.go on REST: page-based pagination for reads,
  and a single Issues.Get to resolve the blocking issue's database ID for
  writes. Preserve the tool surface, self-dependency guard and cross-repo
  support.
- Rewrite the issue dependency tests on the REST mock helpers.
- Regenerate toolsnaps, docs and third-party license files.

Refs #950

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

Author: tommaso-moro

docs/feature-flags.md

@@ -310,14 +310,14 @@ runtime behavior (such as output formatting) won't appear here.
 
 - **issue_dependency_read** - Read issue dependencies
   - **Required OAuth Scopes**: `repo`
-  - `after`: Cursor for pagination. Use the cursor from the previous response. (string, optional)
   - `issue_number`: The number of the issue (number, required)
   - `method`: The read operation to perform on a single issue's dependencies.
     Options are:
     1. get_blocked_by - List the issues that block this issue (this issue is blocked by them).
     2. get_blocking - List the issues that this issue blocks.
      (string, required)
   - `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)
 

docs/insiders-features.md

@@ -105,14 +105,14 @@ The list below is generated from the Go source. It covers tool **inventory and s
 
 - **issue_dependency_read** - Read issue dependencies
   - **Required OAuth Scopes**: `repo`
-  - `after`: Cursor for pagination. Use the cursor from the previous response. (string, optional)
   - `issue_number`: The number of the issue (number, required)
   - `method`: The read operation to perform on a single issue's dependencies.
     Options are:
     1. get_blocked_by - List the issues that block this issue (this issue is blocked by them).
     2. get_blocking - List the issues that this issue blocks.
      (string, required)
   - `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)
 

e2e/e2e_test.go

@@ -18,7 +18,7 @@ import (
 	"github.com/github/github-mcp-server/internal/ghmcp"
 	"github.com/github/github-mcp-server/pkg/github"
 	"github.com/github/github-mcp-server/pkg/translations"
-	gogithub "github.com/google/go-github/v87/github"
+	gogithub "github.com/google/go-github/v89/github"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 	"github.com/stretchr/testify/require"
 )

go.mod

@@ -5,7 +5,7 @@ go 1.25.0
 require (
 	github.com/go-chi/chi/v5 v5.3.0
 	github.com/go-viper/mapstructure/v2 v2.5.0
-	github.com/google/go-github/v87 v87.0.0
+	github.com/google/go-github/v89 v89.0.0
 	github.com/google/jsonschema-go v0.4.3
 	github.com/josephburnett/jd/v2 v2.5.0
 	github.com/lithammer/fuzzysearch v1.1.8

go.sum

@@ -16,8 +16,8 @@ github.com/golang-jwt/jwt/v5 v5.3.1/go.mod h1:fxCRLWMO43lRc8nhHWY6LGqRcf+1gQWArs
 github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
 github.com/google/go-cmp v0.7.0 h1:wk8382ETsv4JYUZwIsn6YpYiWiBsYLSJiTsyBybVuN8=
 github.com/google/go-cmp v0.7.0/go.mod h1:pXiqmnSA92OHEEa9HXL2W4E7lf9JzCmGVUdgjX3N/iU=
-github.com/google/go-github/v87 v87.0.0 h1:9Ck3dcOxWJyfsN8tzdah4YvmqB/7ZsstMglv/PkOsl0=
-github.com/google/go-github/v87 v87.0.0/go.mod h1:hGUoT5pwm/ck5uLL+wroSVQfg8mpe+buxllCcGV4VaM=
+github.com/google/go-github/v89 v89.0.0 h1:35bEK5XoEcF3PZrlVbl9XN63f5BcJRA/UGkxeC9xPg0=
+github.com/google/go-github/v89 v89.0.0/go.mod h1:QLcbU0ipeAqQuR5KSg8c2lql4Qk1EwJ2dWz/0rP4Nho=
 github.com/google/go-querystring v1.2.0 h1:yhqkPbu2/OH+V9BfpCVPZkNmUXhb2gBxJArfhIxNtP0=
 github.com/google/go-querystring v1.2.0/go.mod h1:8IFJqpSRITyJ8QhQ13bmbeMBDfmeEJZD5A0egEOmkqU=
 github.com/google/jsonschema-go v0.4.3 h1:/DBOLZTfDow7pe2GmaJNhltueGTtDKICi8V8p+DQPd0=

internal/ghmcp/server.go

@@ -25,7 +25,7 @@ import (
 	"github.com/github/github-mcp-server/pkg/scopes"
 	"github.com/github/github-mcp-server/pkg/translations"
 	"github.com/github/github-mcp-server/pkg/utils"
-	gogithub "github.com/google/go-github/v87/github"
+	gogithub "github.com/google/go-github/v89/github"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 	"github.com/shurcooL/githubv4"
 )

pkg/errors/error.go

@@ -8,7 +8,7 @@ import (
 	"time"
 
 	"github.com/github/github-mcp-server/pkg/utils"
-	"github.com/google/go-github/v87/github"
+	"github.com/google/go-github/v89/github"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 )
 

pkg/errors/error_test.go

@@ -3,7 +3,7 @@ package errors
 import (
 	"context"
 	"fmt"
-	"github.com/google/go-github/v87/github"
+	"github.com/google/go-github/v89/github"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"

pkg/github/__toolsnaps__/issue_dependency_read_ff_issue_dependencies.snap

@@ -7,10 +7,6 @@
   "description": "Read an issue's dependency relationships in a GitHub repository: the issues that block it (blocked_by) or the issues it blocks (blocking).",
   "inputSchema": {
     "properties": {
-      "after": {
-        "description": "Cursor for pagination. Use the cursor from the previous response.",
-        "type": "string"
-      },
       "issue_number": {
         "description": "The number of the issue",
         "type": "number"
@@ -27,6 +23,11 @@
         "description": "The owner of the repository",
         "type": "string"
       },
+      "page": {
+        "description": "Page number for pagination (min 1)",
+        "minimum": 1,
+        "type": "number"
+      },
       "perPage": {
         "description": "Results per page for pagination (min 1, max 100)",
         "maximum": 100,

pkg/github/actions.go

@@ -17,7 +17,7 @@ import (
 	"github.com/github/github-mcp-server/pkg/scopes"
 	"github.com/github/github-mcp-server/pkg/translations"
 	"github.com/github/github-mcp-server/pkg/utils"
-	"github.com/google/go-github/v87/github"
+	"github.com/google/go-github/v89/github"
 	"github.com/google/jsonschema-go/jsonschema"
 	"github.com/modelcontextprotocol/go-sdk/mcp"
 )