Migrate SKIPIF -> EXTENSIONS (#7138)

This is an automated migration of most SKIPIF extension_loaded checks.

Trim trailing whitespaces and fix code style

Closes GH-5554.

- add ZipArchive::FL_RECOMPRESS, FL_ENCRYPTED, FL_OVERWRITE, FL_LOCAL, FL_CENTRAL constants
- add optional "flags" parameter to ZipArchive::addEmptyDir, addFile and addFromString methods
- ad

- add ZipArchive::FL_RECOMPRESS, FL_ENCRYPTED, FL_OVERWRITE, FL_LOCAL, FL_CENTRAL constants
- add optional "flags" parameter to ZipArchive::addEmptyDir, addFile and addFromString methods
- add "flags" options to ZipArchive::addGlob and addPattern methods
keeping previous behavior having FL_OVERWRITE by default
- add ZipArchive::replaceFile() method

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