The problem with bz2 is the lack of multiple files support. ZIP already supports multiple files (like .tar.bz2).I think that should be great to have transparent ZIP layer at the "include"/"require" level so one could write something like "require './lib/some-arc.par/SomePath/MyClass.php'" but the command-line interface imho should be similar to java i.e.
php -par my-app.par
Personally I would prefer bz2 - at least bzip2 is OpenSource. And packages can be smthing like bcompiler's compiled code - obviously there is no need to change sources of such packages, so they could contain bytecodes.
If we can have native support for ".tar.bz2" I agree with your point of view.
Cristiano Duarte.
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