`$base` is ignored in `$include` directive

The [spec of `$include`](https://www.commonwl.org/v1.2/SchemaSalad.html#Include) says:

> The URI string must be resolved to an absolute URI using the link resolution rules described previously. The URI referenced by `$include` must be loaded as a text data.

Also, the [spec of explicit context](https://www.commonwl.org/v1.2/SchemaSalad.html#Explicit_context) says that `$base` sets the base URI that is used in the [link resolution](https://www.commonwl.org/v1.2/SchemaSalad.html#Link_resolution).

However, `schema-salad-tool` resolves the path relative reference in `$include` directive with the default base URI rather than the value of `$base` field.

# Inputs

`/workspaces/salad/sample.yml`:
```yaml
$base: "https://raw.githubusercontent.com/common-workflow-language/schema_salad/main/"
$graph:
- name: Doc
type: documentation
doc:
$include: lgtm.yml
```

In my understanding, `lgtm.yml` in the `$include` directive is resolved to `https://raw.githubusercontent.com/common-workflow-language/schema_salad/main/lgtm.yml` according to the link resolution rule.

# Expected behavior
`https://raw.githubusercontent.com/common-workflow-language/schema_salad/main/lgtm.yml` is loaded and `$include` directive is replaced with the loaded string as follows:
```console
$ schema-salad-tool --print-pre sample.yml
/usr/local/bin/schema-salad-tool Current version: 8.2.20211222191353
[
{
"name": "https://raw.githubusercontent.com/common-workflow-language/schema_salad/main/#Doc",
"type": "documentation",
"doc": "extraction: \n # Define settings for JavaScript analysis\n ##########################################\n javascript:\n # The `index` step extracts information from the files in the codebase.\n index:\n # Specify a list of files and folders to exclude from extraction.\n exclude:\n - schema_salad/typescript/\n"
}
]
```

# Actual behavior
`lgtm.yml` is resolved to `/workspaces/salad/lgtm.yml` and `schema-salad-tool` fails to load it.
I guess `schema-salad-tool` uses `file:///workspaces/salad/sample.yml` (i.e., the default base URI that is described in the [implied context](https://www.commonwl.org/v1.2/SchemaSalad.html#Implied_context)) as the base URI.

```console
$ schema-salad-tool --print-pre sample.yml
/usr/local/bin/schema-salad-tool Current version: 8.2.20211222191353
loader is 140079248226064
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/schema_salad/fetcher.py", line 86, in fetch_text
urllib.request.url2pathname(str(path)), encoding="utf-8"
FileNotFoundError: [Errno 2] No such file or directory: '/workspaces/salad/lgtm.yml'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 903, in resolve_all
val, base_url + subscope, file_base=file_base, checklinks=False
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 832, in resolve_all
strict_foreign_properties=strict_foreign_properties,
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 501, in resolve_ref
return self.fetch_text(url), CommentedMap()
File "/usr/local/lib/python3.6/dist-packages/schema_salad/fetcher.py", line 92, in fetch_text
raise ValidationException(str(err)) from err
schema_salad.exceptions.ValidationException: [Errno 2] No such file or directory: '/workspaces/salad/lgtm.yml'
failed
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/schema_salad/fetcher.py", line 86, in fetch_text
urllib.request.url2pathname(str(path)), encoding="utf-8"
FileNotFoundError: [Errno 2] No such file or directory: '/workspaces/salad/lgtm.yml'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 903, in resolve_all
val, base_url + subscope, file_base=file_base, checklinks=False
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 832, in resolve_all
strict_foreign_properties=strict_foreign_properties,
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 501, in resolve_ref
return self.fetch_text(url), CommentedMap()
File "/usr/local/lib/python3.6/dist-packages/schema_salad/fetcher.py", line 92, in fetch_text
raise ValidationException(str(err)) from err
schema_salad.exceptions.ValidationException: [Errno 2] No such file or directory: '/workspaces/salad/lgtm.yml'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 947, in resolve_all
val, base_url, file_base=file_base, checklinks=False
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 913, in resolve_all
) from v
schema_salad.exceptions.ValidationException: (140079248226064) (file:///workspaces/salad/sample.yml) Validation error in field doc:
[Errno 2] No such file or directory: '/workspaces/salad/lgtm.yml'
Schema `sample.yml` failed link checking:
(140079248226064) (file:///workspaces/salad/sample.yml) Validation error in position 0:
(140079248226064) (file:///workspaces/salad/sample.yml) Validation error in field doc:
[Errno 2] No such file or directory: '/workspaces/salad/lgtm.yml'
```

# versions
```console
$ schema-salad-tool --version
/usr/local/bin/schema-salad-tool Current version: 8.2.20211222191353
```