Common problems
Class "…\Vendor\…" not found, very early in a request
The prefixed autoloader has not been loaded yet when the code runs. This happens in code that runs before plugins, such as an object-cache.php drop-in or a firewall started from wp-config.php. Turn on include_autoloader so anything that loads Composer's vendor/autoload.php gets the prefixed packages too, or require vendor-prefixed/autoload.php from that code.
Undefined constant such as ACME_MB_CASE_TITLE
A polyfill declares a constant that PHP already defines, and the polyfill's copy was renamed. Turn on the php-constants preset.
A function is undefined after prefixing
Some functions exist in PHP only on certain setups, and libraries ship a polyfill for the others. Strauss-RS leaves the common ones alone (getallheaders(), the apache_* functions and fastcgi_finish_request(), for example). For any other function that your own code or PHP expects to find under its original name, use exclude_from_prefix.functions.
Run explain with the function name to see which setting decided it.
I fixed a setting and my source files still have the wrong name
If update_call_sites already rewrote your files, the old name is gone from them and a new run cannot restore it. Put the files back with git checkout, fix the setting, and run prefix again. See updating your own code.
A theme passes a Collection and my plugin rejects it
After prefixing, Illuminate\Support\Collection in a theme and Acme\Plugin\Vendor\Illuminate\Support\Collection in your plugin are two different classes. Strauss-RS cannot make them interchangeable. Where your plugin takes objects from outside, accept iterable, Traversable or array and wrap the value in your own prefixed class inside your code. Do the same for values you hand back.
A class_alias() from the original name to the prefixed class works only if nothing else has declared the original name, so it is not safe for a library that other plugins or themes might also bundle.
The summary says files were skipped or could not be analysed
Files that Strauss-RS cannot read are reported on stderr. Check that the file is valid PHP. sh bin/strauss-rs.sh analyse path/to/file.php shows what it sees in one file.