dependabot could not clone private repository for swift that located same organization and granted access.

### Is there an existing issue for this?

- [X] I have searched the existing issues

### Package ecosystem

swift

### Package manager version

5.8

### Language version

5.8

### Manifest location and content before the Dependabot update

### `/Package.swift`

repository is `appbrew/try-dependabot-spm`, `appbrew` is the organization name.

```swift
// swift-tools-version: 5.8
// The swift-tools-version declares the minimum version of Swift required to build this package.

import PackageDescription

let package = Package(
name: "try-dependabot-spm",
products: [
// Products define the executables and libraries a package produces, making them visible to other packages.
.library(
name: "try-dependabot-spm",
targets: ["try-dependabot-spm"]),
],
dependencies: [
.package(url: "git@github.com:appbrew/try-dependabot-spm-private.git", exact: "0.0.1"),
],
targets: [
// Targets are the basic building blocks of a package, defining a module or a test suite.
// Targets can depend on other targets in this package and products from dependencies.
.target(
name: "try-dependabot-spm"),
.testTarget(
name: "try-dependabot-spmTests",
dependencies: ["try-dependabot-spm"]),
]
)
```

and `Package.resolved`

```swift
{
"pins" : [
{
"identity" : "try-dependabot-spm-private",
"kind" : "remoteSourceControl",
"location" : "git@github.com:appbrew/try-dependabot-spm-private.git",
"state" : {
"revision" : "e645ddfa48964b5b81ab3fba2976e0989d3d176e",
"version" : "0.0.1"
}
}
],
"version" : 2
}
```

### dependabot.yml content

```yaml
version: 2
updates:
- package-ecosystem: "swift"
directory: "/"
schedule:
interval: "weekly"
```

### Updated dependency

`try-dependabot-spm-private` repo is not yet updated from 0.0.1, so I expect dependabot will not create pull request without error.

### What you expected to see, versus what you actually saw

I expect dependabot will not create pull request without error.

But dependabot will show repository clone error even if grant dependabot access to `try-dependabot-spm-private` repo that describing in [this docs](https://docs.github.com/en/organizations/keeping-your-organization-secure/managing-security-settings-for-your-organization/managing-security-and-analysis-settings-for-your-organization#allowing-dependabot-to-access-private-dependencies).

```
proxy | 2023/09/13 15:22:36 proxy starting, commit: 93c4a893d794d736d84e940a79420e8d1180c0bd
proxy | 2023/09/13 15:22:36 Listening (:1080)
updater | 2023-09-13T15:22:37.794093800 [721527124:main:WARN:src/devices/src/legacy/serial.rs:222] Detached the serial input due to peer close/error.
updater | time="2023-09-13T15:22:40Z" level=info msg="guest starting" commit=b073e069d366dc2f68bb8ef0134feb3c29cacadd
updater | time="2023-09-13T15:22:40Z" level=info msg="starting job..." fetcher_timeout=10m0s job_id=721527124 updater_timeout=45m0s updater_version=3ca52579b79278b4007287c479a40acdee6fb88a-swift
updater | 2023/09/13 15:22:42 INFO Raven 3.1.2 ready to catch errors
updater | 2023/09/13 15:22:43 INFO Starting job processing
proxy | 2023/09/13 15:22:44 [002] GET https://github.com:443/appbrew/try-dependabot-spm/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:44 [002] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:44 [002] 200 https://github.com:443/appbrew/try-dependabot-spm/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:44 [004] POST https://github.com:443/appbrew/try-dependabot-spm/git-upload-pack
proxy | 2023/09/13 15:22:44 [004] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:44 [004] 200 https://github.com:443/appbrew/try-dependabot-spm/git-upload-pack
proxy | 2023/09/13 15:22:44 [006] POST https://github.com:443/appbrew/try-dependabot-spm/git-upload-pack
proxy | 2023/09/13 15:22:44 [006] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:44 [006] 200 https://github.com:443/appbrew/try-dependabot-spm/git-upload-pack
updater | 2023/09/13 15:22:44 INFO Finished job processing
updater | time="2023-09-13T15:22:44Z" level=info msg="task complete" container_id=job-721527124-file-fetcher exit_code=0 job_id=721527124 step=fetcher
updater | 2023/09/13 15:22:46 INFO Raven 3.1.2 ready to catch errors
updater | 2023/09/13 15:22:48 INFO Starting job processing
proxy | 2023/09/13 15:22:50 [008] GET https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:50 [008] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:50 [008] 404 https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:50 [008] * auth'd git request returned 404, retrying without auth
proxy | 2023/09/13 15:22:50 [008] * de-auth'd request returned 401, replacing response
proxy | 2023/09/13 15:22:50 [010] GET https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:50 [010] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:50 [010] 404 https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:50 [010] * auth'd git request returned 404, retrying without auth
proxy | 2023/09/13 15:22:50 [010] * de-auth'd request returned 401, replacing response
proxy | 2023/09/13 15:22:50 [012] GET https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:50 [012] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:51 [012] 404 https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:51 [012] * auth'd git request returned 404, retrying without auth
proxy | 2023/09/13 15:22:51 [012] * de-auth'd request returned 401, replacing response
proxy | 2023/09/13 15:22:51 [014] GET https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:51 [014] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:51 [014] 404 https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:51 [014] * auth'd git request returned 404, retrying without auth
proxy | 2023/09/13 15:22:51 [014] * de-auth'd request returned 401, replacing response
proxy | 2023/09/13 15:22:51 [016] GET https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:51 [016] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:51 [016] 404 https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:51 [016] * auth'd git request returned 404, retrying without auth
proxy | 2023/09/13 15:22:51 [016] * de-auth'd request returned 401, replacing response
proxy | 2023/09/13 15:22:52 [018] GET https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:52 [018] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:52 [018] 404 https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:52 [018] * auth'd git request returned 404, retrying without auth
proxy | 2023/09/13 15:22:52 [018] * de-auth'd request returned 401, replacing response
proxy | 2023/09/13 15:22:52 [020] GET https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:52 [020] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:52 [020] 404 https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:52 [020] * auth'd git request returned 404, retrying without auth
proxy | 2023/09/13 15:22:52 [020] * de-auth'd request returned 401, replacing response
proxy | 2023/09/13 15:22:52 [022] GET https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:52 [022] * authenticating git server request (host: github.com)
proxy | 2023/09/13 15:22:52 [022] 404 https://github.com:443/appbrew/try-dependabot-spm-private.git/info/refs?service=git-upload-pack
proxy | 2023/09/13 15:22:52 [022] * auth'd git request returned 404, retrying without auth
proxy | 2023/09/13 15:22:52 [022] * de-auth'd request returned 401, replacing response
updater | 2023/09/13 15:22:53 ERROR Fetching git@github.com:appbrew/try-dependabot-spm-private.git
updater | warning: 'try-dependabot-spm-private': skipping cache due to an error: Failed to clone repository git@github.com:appbrew/try-dependabot-spm-private.git:
updater | Cloning into bare repository '/home/dependabot/.cache/org.swift.swiftpm/repositories/try-dependabot-spm-private-664e0590'...
updater | fatal: could not read Password for 'https://git@github.com': terminal prompts disabled
updater | Fetching git@github.com:appbrew/try-dependabot-spm-private.git
updater | warning: 'try-dependabot-spm-private': skipping cache due to an error: Failed to clone repository git@github.com:appbrew/try-dependabot-spm-private.git:
updater | Cloning into bare repository '/home/dependabot/.cache/org.swift.swiftpm/repositories/try-dependabot-spm-private-664e0590'...
updater | fatal: could not read Password for 'https://git@github.com': terminal prompts disabled
updater | error: Failed to clone repository git@github.com:appbrew/try-dependabot-spm-private.git:
updater | Cloning into bare repository '/home/dependabot/dependabot-updater/repo/.build/repositories/try-dependabot-spm-private-664e0590'...
updater | fatal: could not read Password for 'https://git@github.com': terminal prompts disabled
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/common/lib/dependabot/shared_helpers.rb:343:in `run_shell_command'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/swift/lib/dependabot/swift/file_parser/dependency_parser.rb:38:in `formatted_deps'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/swift/lib/dependabot/swift/file_parser/dependency_parser.rb:24:in `block (2 levels) in parse'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/common/lib/dependabot/shared_helpers.rb:194:in `with_git_configured'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/swift/lib/dependabot/swift/file_parser/dependency_parser.rb:23:in `block in parse'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/common/lib/dependabot/shared_helpers.rb:41:in `block in in_a_temporary_repo_directory'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/common/lib/dependabot/shared_helpers.rb:41:in `chdir'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/common/lib/dependabot/shared_helpers.rb:41:in `in_a_temporary_repo_directory'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/swift/lib/dependabot/swift/file_parser/dependency_parser.rb:20:in `parse'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/swift/lib/dependabot/swift/file_parser.rb:17:in `parse'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:99:in `parse_files!'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:88:in `initialize'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:21:in `new'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:21:in `create_from_job_definition'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/dependabot-updater/lib/dependabot/update_files_command.rb:16:in `perform_job'
updater | 2023/09/13 15:22:53 ERROR /home/dependabot/dependabot-updater/lib/dependabot/base_command.rb:52:in `run'
updater | 2023/09/13 15:22:53 ERROR bin/update_files.rb:23:in `'
updater | 2023/09/13 15:22:53 INFO Sending event dc0968eb0ab240f2bc71de1549ff1a5a to Sentry
proxy | 2023/09/13 15:22:53 [024] POST https://sentry.io:443/api/1451818/store/
proxy | 2023/09/13 15:22:53 [024] 200 https://sentry.io:443/api/1451818/store/
updater | 2023/09/13 15:22:54 INFO Finished job processing
updater | 2023/09/13 15:22:54 INFO Results:
updater | Dependabot encountered '1' error(s) during execution, please check the logs for more details.
updater | +---------------+
updater | | Errors |
updater | +---------------+
updater | | unknown_error |
updater | +---------------+
updater | time="2023-09-13T15:22:54Z" level=info msg="task complete" container_id=job-721527124-updater exit_code=0 job_id=721527124 step=updater
```

### Native package manager behavior

no output without error.

```
$ swift package resolve
$
```

### Images of the diff or a link to the PR, issue, or logs

_No response_

### Smallest manifest that reproduces the issue

_No response_

Start with swift/lib/dependabot/swift/file_parser/dependency_parser.rb and the shared_helpers.rb calls shown in the stack trace. Reproduce the clone failure using the provided Package.swift, Package.resolved, and dependabot.yml, then trace how the authenticated private dependency URL is handled. Done means an accessible private Swift dependency can be fetched without the password prompt or clone error, with regression coverage for this organization-scoped case.

Written by the indexing model from the issue text.