Standalone System - bring default Civi::paths factories in line with installer defaults

[ufundo]

Overview

#29960 updated the default Standalone directory structure in a somewhat brute force way - by setting path overrides in the installer, that are then written out into civicrm.settings.php

This returns to CRM_Utils_System_Standalone to bring the underlying defaults in line with the directory structure changes.

Before

civicrm.settings.php contains many path overrides

Even though they just reiterate our intended defaults, removing them will cause your system to crash because the underlying defaults are different.

After

The above overrides will all still be set by the installer.

But if you haven't diverged from the default, those lines can be safely removed.

This is a helpful step to reduce reliance on civicrm.settings.php in a portable context (e.g. Docker container).

Technical Details

In many cases having these paths fixed in your civicrm.settings.php makes sense: if the defaults ever change in the codebase, your folders will still be where they were at install time, so the "frozen" copy of the paths is helpful.

But we shouldn't rely on the settings file to provide defaults.

Some extraneous bootstap code in CRM_Utils_System_Standalone is removed which otherwise caused a crash by trying to read directly $civicrm_paths. The line is trying to reload the autoloader - which is always handled in Standalone context by civicrm.standalone.php.

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[ufundo]

There's some crossover between this and #31150

I will attempt to take the paths stuff out of that PR because this one is a more logical package 📦

[wmortada]

There's some crossover between this and #31150

More than a little crossover. I'd say they are identical! 😉

[ufundo]

(just to note the upgrade tests are failing for other reasons)

[ufundo]

Oops, thanks @wmortada !

The PR with not as much crossover but some is #31127

I think it would preferable to merge this first, and rebase 31127 onto this.

[colemanw]

Better to get rid of the cruft now than later.