fix(github): combine --repository and --organization flags for scan scoping (#10005)

Co-authored-by: Andoni Alonso <14891798+andoniaf@users.noreply.github.com>

docs/user-guide/providers/github/authentication.mdx

@@ -38,6 +38,7 @@ GitHub has deprecated Personal Access Tokens (classic) in favor of fine-grained
 
 4. **Configure Token Settings**
     - **Token name**: Give your token a descriptive name (e.g., "Prowler Security Scanner")
+    - **Resource owner**: Select the account that owns the resources to scan — either a personal account or a specific organization
     - **Expiration**: Set an appropriate expiration date (recommended: 90 days or less)
     - **Repository access**: Choose "All repositories" or "Only select repositories" based on your needs
 
@@ -56,11 +57,11 @@ GitHub has deprecated Personal Access Tokens (classic) in favor of fine-grained
         - **Metadata**: Read-only access
         - **Pull requests**: Read-only access
 
-    - **Organization permissions:**
+    - **Organization permissions** (available when an organization is selected as Resource Owner):
         - **Administration**: Read-only access
         - **Members**: Read-only access
 
-    - **Account permissions:**
+    - **Account permissions** (available when a personal account is selected as Resource Owner):
         - **Email addresses**: Read-only access
 
 6. **Copy and Store the Token**

docs/user-guide/providers/github/getting-started-github.mdx

@@ -54,7 +54,7 @@ title: 'Getting Started with GitHub'
 </Tabs>
 ## Prowler CLI
 
-### Automatic Login Method Detection
+### Authentication
 
 If no login method is explicitly provided, Prowler will automatically attempt to authenticate using environment variables in the following order of precedence:
 
@@ -68,15 +68,15 @@ Ensure the corresponding environment variables are set up before running Prowler
 </Note>
 For more details on how to set up authentication with GitHub, see [Authentication > GitHub](/user-guide/providers/github/authentication).
 
-### Personal Access Token (PAT)
+#### Personal Access Token (PAT)
 
-Use this method by providing your personal access token directly.
+Use this method by providing a personal access token directly.
 
 ```console
 prowler github --personal-access-token pat
 ```
 
-### OAuth App Token
+#### OAuth App Token
 
 Authenticate using an OAuth app token.
 
@@ -84,9 +84,62 @@ Authenticate using an OAuth app token.
 prowler github --oauth-app-token oauth_token
 ```
 
-### GitHub App Credentials
+#### GitHub App Credentials
+
 Use GitHub App credentials by specifying the App ID and the private key path.
 
 ```console
 prowler github --github-app-id app_id --github-app-key-path app_key_path
 ```
+
+### Scan Scoping
+
+By default, Prowler scans all repositories accessible to the authenticated user or organization. To limit the scan to specific repositories or organizations, use the following flags.
+
+#### Scanning Specific Repositories
+
+To restrict the scan to one or more repositories, use the `--repository` flag followed by the repository name(s) in `owner/repo-name` format:
+
+```console
+prowler github --repository owner/repo-name
+```
+
+To scan multiple repositories, specify them as space-separated arguments:
+
+```console
+prowler github --repository owner/repo-name-1 owner/repo-name-2
+```
+
+#### Scanning Specific Organizations
+
+To restrict the scan to one or more organizations or user accounts, use the `--organization` flag:
+
+```console
+prowler github --organization my-organization
+```
+
+To scan multiple organizations, specify them as space-separated arguments:
+
+```console
+prowler github --organization org-1 org-2
+```
+
+#### Scanning Specific Repositories Within an Organization
+
+To scan specific repositories within an organization, combine the `--organization` and `--repository` flags. The `--organization` flag qualifies unqualified repository names automatically:
+
+```console
+prowler github --organization my-organization --repository my-repo
+```
+
+This scans only `my-organization/my-repo`. Fully qualified repository names (`owner/repo-name`) are also supported alongside `--organization`:
+
+```console
+prowler github --organization my-org --repository my-repo other-owner/other-repo
+```
+
+In this case, `my-repo` is qualified as `my-org/my-repo`, while `other-owner/other-repo` is used as-is.
+
+<Note>
+The `--repository` and `--organization` flags can be combined with any authentication method.
+</Note>

prowler/CHANGELOG.md

@@ -2,6 +2,14 @@
 
 All notable changes to the **Prowler SDK** are documented in this file.
 
+## [5.18.2] (Prowler UNRELEASED)
+
+### 🐞 Fixed
+
+- `--repository` and `--organization` flags combined interaction in GitHub provider, qualifying unqualified repository names with organization [(#10001)](https://github.com/prowler-cloud/prowler/pull/10001)
+
+---
+
 ## [5.18.0] (Prowler v5.18.0)
 
 ### 🚀 Added

prowler/providers/github/services/repository/repository_service.py

@@ -121,15 +121,22 @@ class Repository(GithubService):
                     )
                 ):
                     if self.provider.repositories:
-                        logger.info(
-                            f"Filtering for specific repositories: {self.provider.repositories}"
-                        )
+                        qualified_repos = []
                         for repo_name in self.provider.repositories:
-                            if not self._validate_repository_format(repo_name):
+                            if self._validate_repository_format(repo_name):
+                                qualified_repos.append(repo_name)
+                            elif self.provider.organizations:
+                                for org_name in self.provider.organizations:
+                                    qualified_repos.append(f"{org_name}/{repo_name}")
+                            else:
                                 logger.warning(
                                     f"Repository name '{repo_name}' should be in 'owner/repo-name' format. Skipping."
                                 )
-                                continue
+
+                        logger.info(
+                            f"Filtering for specific repositories: {qualified_repos}"
+                        )
+                        for repo_name in qualified_repos:
                             try:
                                 repo = client.get_repo(repo_name)
                                 self._process_repository(repo, repos)
@@ -138,7 +145,7 @@ class Repository(GithubService):
                                     error, "accessing repository", repo_name
                                 )
 
-                    if self.provider.organizations:
+                    elif self.provider.organizations:
                         logger.info(
                             f"Filtering for repositories in organizations: {self.provider.organizations}"
                         )

skills/prowler-changelog/SKILL.md

@@ -74,6 +74,7 @@ allowed-tools: Read, Edit, Write, Glob, Grep, Bash
 - One entry per PR (can link multiple PRs for related changes)
 - No period at the end
 - Do NOT start with redundant verbs (section header already provides the action)
+- **CRITICAL: Preserve section order** — when adding a new section to the UNRELEASED block, insert it in the correct position relative to existing sections (Added → Changed → Deprecated → Removed → Fixed → Security). Never append a new section at the top or bottom without checking order
 
 ### Semantic Versioning Rules
 
@@ -177,6 +178,13 @@ This maintains chronological order within each section (oldest at top, newest at
 ### Bad Entries
 
 ```markdown
+# BAD - Wrong section order (Fixed before Added)
+### 🐞 Fixed
+- Some bug fix [(#123)](...)
+
+### 🚀 Added
+- Some new feature [(#456)](...)
+
 - Fixed bug.                              # Too vague, has period
 - Added new feature for users             # Missing PR link, redundant verb
 - Add search bar [(#123)]                 # Redundant verb (section already says "Added")

tests/providers/github/services/repository/repository_service_test.py

@@ -245,19 +245,61 @@ class Test_Repository_Scoping:
         self.mock_repo2.get_branch.side_effect = Exception("404 Not Found")
         self.mock_repo2.get_dependabot_alerts.side_effect = Exception("404 Not Found")
 
-    def test_combined_repository_and_organization_scoping(self):
-        """Test that both repository and organization scoping can be used together"""
+    def test_qualified_repo_with_organization_skips_org_fetch(self):
+        """Test that a fully qualified repo with --organization does not fetch all org repos"""
         provider = set_mocked_github_provider()
         provider.repositories = ["owner1/repo1"]
         provider.organizations = ["org2"]
 
         mock_client = MagicMock()
-        # Repository lookup
         mock_client.get_repo.return_value = self.mock_repo1
-        # Organization lookup
-        mock_org = MagicMock()
-        mock_org.get_repos.return_value = [self.mock_repo2]
-        mock_client.get_organization.return_value = mock_org
+
+        with patch(
+            "prowler.providers.github.services.repository.repository_service.GithubService.__init__"
+        ):
+            repository_service = Repository(provider)
+            repository_service.clients = [mock_client]
+            repository_service.provider = provider
+
+            repos = repository_service._list_repositories()
+
+            assert len(repos) == 1
+            assert 1 in repos
+            assert repos[1].name == "repo1"
+            mock_client.get_repo.assert_called_once_with("owner1/repo1")
+            mock_client.get_organization.assert_not_called()
+
+    def test_unqualified_repo_qualified_with_organization(self):
+        """Test that an unqualified repo name is qualified with the organization"""
+        provider = set_mocked_github_provider()
+        provider.repositories = ["repo1"]
+        provider.organizations = ["owner1"]
+
+        mock_client = MagicMock()
+        mock_client.get_repo.return_value = self.mock_repo1
+
+        with patch(
+            "prowler.providers.github.services.repository.repository_service.GithubService.__init__"
+        ):
+            repository_service = Repository(provider)
+            repository_service.clients = [mock_client]
+            repository_service.provider = provider
+
+            repos = repository_service._list_repositories()
+
+            assert len(repos) == 1
+            assert 1 in repos
+            assert repos[1].name == "repo1"
+            mock_client.get_repo.assert_called_once_with("owner1/repo1")
+
+    def test_unqualified_repo_qualified_with_multiple_organizations(self):
+        """Test that an unqualified repo is qualified with each organization"""
+        provider = set_mocked_github_provider()
+        provider.repositories = ["repo1"]
+        provider.organizations = ["org1", "org2"]
+
+        mock_client = MagicMock()
+        mock_client.get_repo.side_effect = [self.mock_repo1, self.mock_repo2]
 
         with patch(
             "prowler.providers.github.services.repository.repository_service.GithubService.__init__"
@@ -269,12 +311,56 @@ class Test_Repository_Scoping:
             repos = repository_service._list_repositories()
 
             assert len(repos) == 2
-            assert 1 in repos
-            assert 2 in repos
-            assert repos[1].name == "repo1"
-            assert repos[2].name == "repo2"
-            mock_client.get_repo.assert_called_once_with("owner1/repo1")
-            mock_client.get_organization.assert_called_once_with("org2")
+            mock_client.get_repo.assert_any_call("org1/repo1")
+            mock_client.get_repo.assert_any_call("org2/repo1")
+
+    def test_unqualified_repo_without_organization_is_skipped(self):
+        """Test that an unqualified repo without --organization is skipped with a warning"""
+        provider = set_mocked_github_provider()
+        provider.repositories = ["repo1"]
+        provider.organizations = []
+
+        mock_client = MagicMock()
+
+        with patch(
+            "prowler.providers.github.services.repository.repository_service.GithubService.__init__"
+        ):
+            repository_service = Repository(provider)
+            repository_service.clients = [mock_client]
+            repository_service.provider = provider
+
+            with patch(
+                "prowler.providers.github.services.repository.repository_service.logger"
+            ) as mock_logger:
+                repos = repository_service._list_repositories()
+
+                assert len(repos) == 0
+                mock_logger.warning.assert_called_with(
+                    "Repository name 'repo1' should be in 'owner/repo-name' format. Skipping."
+                )
+                mock_client.get_repo.assert_not_called()
+
+    def test_mixed_qualified_and_unqualified_repos_with_organization(self):
+        """Test mix of qualified and unqualified repos with --organization"""
+        provider = set_mocked_github_provider()
+        provider.repositories = ["repo1", "owner2/repo2"]
+        provider.organizations = ["org1"]
+
+        mock_client = MagicMock()
+        mock_client.get_repo.side_effect = [self.mock_repo1, self.mock_repo2]
+
+        with patch(
+            "prowler.providers.github.services.repository.repository_service.GithubService.__init__"
+        ):
+            repository_service = Repository(provider)
+            repository_service.clients = [mock_client]
+            repository_service.provider = provider
+
+            repos = repository_service._list_repositories()
+
+            assert len(repos) == 2
+            mock_client.get_repo.assert_any_call("org1/repo1")
+            mock_client.get_repo.assert_any_call("owner2/repo2")
 
 
 class Test_Repository_Validation: