Yarn 2 protocols result in Dependabot error

### Is there an existing issue for this?

- [X] I have searched the existing issues

### Package ecosystem

npm

### Package manager version

Yarn 3.1.1

### Language version

Node.js 16.13.2

### Manifest location and content before the Dependabot update

_No response_

### dependabot.yml content

```yml
version: 2
updates:
  - package-ecosystem: npm
    directory: '/'
    schedule:
      interval: weekly
      day: saturday
    open-pull-requests-limit: 10
    target-branch: dev
    commit-message:
      prefix: fix
      prefix-development: chore
      include: scope
    allow:
      - dependency-type: development
      - dependency-name: '@lingui/*'
      - dependency-name: '@sentry/*'
      - dependency-name: 'next'
    ignore:
      - dependency-name: '~'
      - dependency-name: e2e
      - dependency-name: react-is
      - dependency-name: typescript
```

### Updated dependency

_No response_

### What you expected to see, versus what you actually saw

We make use of [Yarn 2 protocols](https://yarnpkg.com/protocols), specifically the `link:` protocol to get *native* module aliases (at the package manager level), so we don't need further tooling (Babel module resolver, etc.). We can then import like so:

```js
// resolves to our <root>/e2e folder
import pages from 'e2e/pages.fixture.mjs'

// resolves to our <root>/src folder
import Widget from '~/components/widgets/Widget'
import isEmpty from '~/helpers/isEmpty'
```

These links are defined in our `package.json` among other dependencies:

```json
{
  "dependencies": {
    "date-fns": "^2.28.0",
    "e2e": "link:./e2e",
    "~": "link:./src"
  }
}
```

Dependabot will choke on these when trying to fetch them. As noted above, I tried to ignore them in our `dependabot.yml`, which didn't work.

### Native package manager behavior

_No response_

### Images of the diff or a link to the PR, issue, or logs

This is the error we see in our Dependency graph:

![image](https://user-images.githubusercontent.com/14262802/201308679-879057ee-2d30-4684-867d-21ee4bbb42c0.png)

Here are the update logs we see:

```
  proxy | time="2022-11-10T20:48:04Z" level=info msg="proxy starting" commit=fa80f718f24b195d66d5537781a77f0a8e8cee62
  proxy | 2022/11/10 20:48:04 Listening (:1080)
updater | 2022-11-10T20:48:04.491575147 [507683626:main:WARN:src/devices/src/legacy/serial.rs:214] Detached the serial input due to peer close/error.
updater | time="2022-11-10T20:48:06Z" level=info msg="guest starting" commit=42441b355753c42573b16dc1d5c0da5de9bb45b3
updater | time="2022-11-10T20:48:06Z" level=info msg="starting job..." fetcher_timeout=5m0s job_id=507683626 updater_timeout=45m0s updater_version=cf448a99d35d7956f4c64b8249029324c9627a91
updater | I, [2022-11-10T20:48:07.736537 #8]  INFO -- sentry: ** [Raven] Raven 3.1.2 ready to catch errors
updater | To use retry middleware with Faraday v2.0+, install `faraday-retry` gem
updater | INFO <job_507683626> Starting job processing
  proxy | 2022/11/10 20:48:09 [002] GET https://github.com:443/monitora-media/monitora-frontend/info/refs?service=git-upload-pack
  proxy | 2022/11/10 20:48:09 [002] * authenticating git server request (host: github.com)
  proxy | 2022/11/10 20:48:09 [002] 200 https://github.com:443/monitora-media/monitora-frontend/info/refs?service=git-upload-pack
  proxy | 2022/11/10 20:48:10 [004] POST https://github.com:443/monitora-media/monitora-frontend/git-upload-pack
  proxy | 2022/11/10 20:48:10 [004] * authenticating git server request (host: github.com)
  proxy | 2022/11/10 20:48:10 [004] 200 https://github.com:443/monitora-media/monitora-frontend/git-upload-pack
  proxy | 2022/11/10 20:48:10 [006] POST https://github.com:443/monitora-media/monitora-frontend/git-upload-pack
  proxy | 2022/11/10 20:48:10 [006] * authenticating git server request (host: github.com)
  proxy | 2022/11/10 20:48:10 [006] 200 https://github.com:443/monitora-media/monitora-frontend/git-upload-pack
updater | ERROR <job_507683626> Error during file fetching; aborting
updater | INFO <job_507683626> Finished job processing
updater | INFO Results:
updater | Dependabot encountered '1' error(s) during execution, please check the logs for more details.
updater | time="2022-11-10T20:48:15Z" level=info msg="task complete" container_id=job-507683626-file-fetcher exit_code=0 job_id=507683626 step=fetcher
updater | time="2022-11-10T20:48:15Z" level=warning msg="failed during fetch, skipping updater" job_id=507683626
```

### Smallest manifest that reproduces the issue

#### Files

*the_whole_thing.patch* (separate files below)
```patch
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..c01e06f
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,13 @@
+node_modules
+
+# Yarn
+.yarn/*
+!.yarn/patches
+!.yarn/plugins
+!.yarn/releases
+!.yarn/sdks
+!.yarn/versions
+
+# Zero-Installs disabled
+# !.yarn/cache
+.pnp.*
diff --git a/.yarnrc.yml b/.yarnrc.yml
new file mode 100644
index 0000000..3186f3f
--- /dev/null
+++ b/.yarnrc.yml
@@ -0,0 +1 @@
+nodeLinker: node-modules
diff --git a/index.mjs b/index.mjs
new file mode 100644
index 0000000..f6e69b5
--- /dev/null
+++ b/index.mjs
@@ -0,0 +1,4 @@
+import { isToday } from "date-fns";
+import { isYesterday } from "~/util/isYesterday.mjs";
+
+console.log(isToday(new Date()), isYesterday(new Date()));
diff --git a/package.json b/package.json
new file mode 100644
index 0000000..54e81fe
--- /dev/null
+++ b/package.json
@@ -0,0 +1,8 @@
+{
+  "name": "yarn2dependabot",
+  "packageManager": "yarn@3.2.4",
+  "dependencies": {
+    "date-fns": "^2.29.3",
+    "~": "link:./src"
+  }
+}
diff --git a/src/util/isYesterday.mjs b/src/util/isYesterday.mjs
new file mode 100644
index 0000000..3d4149a
--- /dev/null
+++ b/src/util/isYesterday.mjs
@@ -0,0 +1 @@
+export { isYesterday } from "date-fns";
```

*src/util/isYesterday.mjs*
```js
export { isYesterday } from "date-fns";
```

*.yarnrc.yml*
```yml
nodeLinker: node-modules
```

*index.mjs*
```js
import { isToday } from "date-fns";
import { isYesterday } from "~/util/isYesterday.mjs";

console.log(isToday(new Date()), isYesterday(new Date()));
```

*package.json*
```json
{
  "name": "yarn2dependabot",
  "packageManager": "yarn@3.2.4",
  "dependencies": {
    "date-fns": "^2.29.3",
    "~": "link:./src"
  }
}
```

#### Usage

Put the above files in a new folder, or apply the patch to a new empty repo and run:

```sh
$ yarn
$ node index.mjs # should output:
# true false
```

Running a Dependabot update on this project should result in the error.

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Yarn 2 protocols result in Dependabot error #6107

Is there an existing issue for this?

Package ecosystem

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Manifest location and content before the Dependabot update

dependabot.yml content

Updated dependency

What you expected to see, versus what you actually saw

Native package manager behavior

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

Smallest manifest that reproduces the issue

Files

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Yarn 2 protocols result in Dependabot error #6107

Description

Is there an existing issue for this?

Package ecosystem

Package manager version

Language version

Manifest location and content before the Dependabot update

dependabot.yml content

Updated dependency

What you expected to see, versus what you actually saw

Native package manager behavior

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

Smallest manifest that reproduces the issue

Files

Usage

Metadata

Metadata

Assignees

Labels

Type

Fields

Projects

Milestone

Relationships

Development

Issue actions