Fix install error for some paths

[singular0]

Instead of str_replace, which may, instead of truncating lead directory from the path, replace some random inner part of it, use substr to remove it.

[LukeTowers]

@singular0 would you be willing to add a test case for this?

[singular0]

@LukeTowers well, this will not fit into modules/system/tests/classes/FileManifestTest.php, as to test you have to initialize FileManifest with $root path that is substring of inner files paths (like "/test"). not sure how to proceed here. create separate TestCase for this in a separate file?

[LukeTowers]

@singular0 you can put it in the same test, you would just initialize a new local instance of FileManifest instead of using the pre-initialized instance.

[singular0]

@LukeTowers ok, so i was unable to create direct test of the #988 itself as github runner (as well as my local macos system integrity protection) does not allow to create directories in /. the best thing i could come up with is the test that proves changed FileManifest->getFilename() to work correctly.