Migrate skip checks to --EXTENSIONS--, p4

For rationale, see #6787

Extensions migrated in part 4:
* simplexml
* skeleton
* soap
* spl
* sqlite3
* sysvmsg

Migrate skip checks to --EXTENSIONS--, p4

For rationale, see #6787

Extensions migrated in part 4:
* simplexml
* skeleton
* soap
* spl
* sqlite3
* sysvmsg
* sysvsem
* tidy - also removed a check for an ancient dependency version

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Fix #63575: Root elements are not properly cloned

Cloning of root elements has to preserve that property, so they require
some special treatment.