You can not avoid the installation of the ispconfig pacakges.
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than to overwrite them with yours.
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ISPConfig does not overwrite any package of the linux distribution.
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In general I don't think that software that is widely available in packages for all major distributions should be force-compiled on a machine with an administration panel.
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These packages are not availabe by all supported linux distributions with the needed compile options. Also the packages in ISPConfig are newer then the packages in most linux distributions and its always a good idea to use the latest antivirus scanner and not a old one were just securiity issues were fixed.
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I see you just released a beta version of ISPConfig 3, do you continue this practice with that version?
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ISPConfig 3 uses only system packages. But it might be nescessary to offer custom repositorys for some distributions later that do not offer up to date packages for older releases.
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