The new `from_file` field contains the name of the input directory even with `--strip-root`

### Description

I'd expect the value of the new `from_file` field inside the JSON's `matches` object to be a path relative to the input directory (if `--strip-root` is given). Instead, it is a relative path, but it contains the name of the input directory.

### How To Reproduce

Using ScanCode 32.1.0, run a scan on the files mentioned at #3648. This gets you

```
"headers": [
{
"tool_name": "scancode-toolkit",
"tool_version": "32.1.0",
"options": {
"input": [
"/home/sebastian/Downloads/files"
],
"--copyright": true,
"--info": true,
"--json-pp": "scancode-result.json",
"--license": true,
"--strip-root": true,
"--timeout": "300.0"
},
```

```
"files": [
{
"path": "COPYING",
"type": "file",
"name": "COPYING",
"base_name": "COPYING",
"extension": "",
"size": 2775,
"date": "2024-01-29",
"sha1": "66933e63e70616b43f1dc60340491f8e050eedfd",
"md5": "97d554a32881fee0aa283d96e47cb24a",
"sha256": "bcb02973ef6e87ea73d331b3a80df7748407f17efdb784b61b47e0e610d3bb5c",
"mime_type": "text/plain",
"file_type": "ASCII text",
"programming_language": null,
"is_binary": false,
"is_text": true,
"is_archive": false,
"is_media": false,
"is_source": false,
"is_script": false,
"detected_license_expression": "public-domain AND lgpl-2.1-plus AND gpl-2.0-plus AND (public-domain AND gpl-2.0-plus AND gpl-3.0-plus) AND (other-permissive AND other-copyleft) AND public-domain-disclaimer AND lgpl-2.1",
"detected_license_expression_spdx": "LicenseRef-scancode-public-domain AND LGPL-2.1-or-later AND GPL-2.0-or-later AND (LicenseRef-scancode-public-domain AND GPL-2.0-or-later AND GPL-3.0-or-later) AND (LicenseRef-scancode-other-permissive AND LicenseRef-scancode-other-copyleft) AND LicenseRef-scancode-public-domain-disclaimer AND LGPL-2.1-only",
"license_detections": [
{
"license_expression": "public-domain AND lgpl-2.1-plus AND gpl-2.0-plus AND (public-domain AND gpl-2.0-plus AND gpl-3.0-plus) AND (other-permissive AND other-copyleft) AND public-domain-disclaimer AND lgpl-2.1",
"license_expression_spdx": "LicenseRef-scancode-public-domain AND LGPL-2.1-or-later AND GPL-2.0-or-later AND (LicenseRef-scancode-public-domain AND GPL-2.0-or-later AND GPL-3.0-or-later) AND (LicenseRef-scancode-other-permissive AND LicenseRef-scancode-other-copyleft) AND LicenseRef-scancode-public-domain-disclaimer AND LGPL-2.1-only",
"matches": [
{
"license_expression": "public-domain",
"spdx_license_expression": "LicenseRef-scancode-public-domain",
"from_file": "files/COPYING",
```

So compare

"path": "COPYING",

to

"from_file": "files/COPYING",

which makes it unnecessary hard to check whether a given finding is actually just a reference or not by comparing whether both fields point to the same path.

I propose to either:
- apply a fix for both fields to contain comparable paths,
- only add `from_file` at all if it's pointing to a different file than `path`,
- add a dedicated `is_reference` field to yet more easily filter out findings that are just references to other scanned files.

### System configuration

* What OS are you running on? Fedora Linux 39
* What version of scancode-toolkit was used to generate the scan file? 32.1.0
* What installation method was used to install/run scancode? pip