(cdk pipelines): primary output directory `root/cdk.out` generates errors since notices release

### What is the problem?

We observe in the default cdk pipeline:
```
Failed to load notices from cache: Error: ENOENT: no such file or directory, open '/root/.cdk/cache/notices.json'
Error on request: Error: read ETIMEDOUT
Notices refreshed
Error on request: Error: read ETIMEDOUT
Failed to get tree.json file: Error: cdk.out/tree.json: ENOTDIR: not a directory, open 'cdk.out/tree.json'
```
Note, we have the `cdk root` of our project in /infrastructure folder. That is specified in code:
```js
primaryOutputDirectory: "infrastructure/cdk.out",
```

It does not result in error, just in a very long wait and then succesful exit.

### Reproduction Steps

```js
const pipeline = new pipelines.CodePipeline(
this,
"niceName",
{
pipelineName: "niceName",
crossAccountKeys: true,
synth: new pipelines.CodeBuildStep("SynthStep", {
input: remote,
commands: [
"cd infrastructure",
"npm ci",
"npm run test",
"npm run build",
"npx cdk synth",
],
primaryOutputDirectory: "infrastructure/cdk.out",
}),
codeBuildDefaults: {
vpc: <...>,
subnetSelection: { subnets: <...> },
partialBuildSpec: codebuild.BuildSpec.fromObject({
phases: {
install: {
"runtime-versions": {
nodejs: "14.x",
},
},
pre_build: {
commands: ["n 16"],
},
},
}),
rolePolicy: [
new iam.PolicyStatement({
actions: ["<...>:<...>"],
resources: ["<...>"],
}),
],
},
}
);
```

### What did you expect to happen?

Pipeline result:
```
Time taken 30s blahblah :D
```

### What actually happened?

```
Failed to load notices from cache: Error: ENOENT: no such file or directory, open '/root/.cdk/cache/notices.json'
Error on request: Error: read ETIMEDOUT
Notices refreshed
Error on request: Error: read ETIMEDOUT
Failed to get tree.json file: Error: cdk.out/tree.json: ENOTDIR: not a directory, open 'cdk.out/tree.json'
```

### CDK CLI Version

2.13.0

### Framework Version

_No response_

### Node.js Version

17

### OS

MacOs

### Language

Typescript

### Language Version

TS 4

### Other information

_No response_

Start with the CodePipeline and CodeBuildStep configuration shown in the issue, especially the `cd infrastructure` command and `primaryOutputDirectory: "infrastructure/cdk.out"`. Reproduce the synth using the listed commands and inspect how the output directory is resolved; done means the pipeline completes without the `cdk.out/tree.json` ENOTDIR error and without the excessive wait.

Written by the indexing model from the issue text.