depends: Various config.site.in improvements and linting #20359

Previously, if ./configure was invoked with:

```
$ env CONFIG_SITE=depends/x86_64-pc-linux-gnu/share/config.site ./configure
```

Where $CONFIG_SITE was a relative path, ./configure would fail with the
following misleading output:

```
checking for boostlib >= 1.58.0 (105800)... yes
checking whether the Boost::System library is available... yes
configure: error: Could not find a version of the Boost::System library!
```

Fully resolving depends_prefix in config.site.in fixes this. To make
sure that there are no other side effects I ran a diff on the
config.status generated by:

1. The scripts prior to this change with CONFIG_SITE set to a full path:
       env CONFIG_SITE=$PWD/depends/x86_64-pc-linux-gnu/share/config.site ./configure
2. The scripts after this change with CONFIG_SITE set to a relative path:
       env CONFIG_SITE=depends/x86_64-pc-linux-gnu/share/config.site ./configure

And it looks good!

Diff: https://paste.sr.ht/~dongcarl/95b469fbc555c128046e85723d87a9082a754f6b

Files like config.site.in are not referenced by any other script in our
tree, so we need to mark it manually with a "shellcheck shell="
directive and make sure that shellcheck is run on them.

Previously, when running ./configure:

1. With CONFIG_SITE pointed to our depends config.site.in, and
2. PYTHONPATH was not set either in the environment or by the user

The configure would output something like:

PYTHONPATH='depends/x86_64-pc-linux-gnu/share/../native/lib/python3/dist-packages:'

When we really mean:

PYTHONPATH='depends/x86_64-pc-linux-gnu/share/../native/lib/python3/dist-packages'

...without the colon

This change makes sure that:

1. There's no trailing colon, and
2. We use the $PATH_SEPARATOR variable instead of a colon