update BEAUti and wiki to use term "Package"

[tgvaughan]

This is related to issue 32 .

I have replaced most of "Add-on(s)" into "Plugin(s)" in wiki, except of 2 wiki pages that contain GUI screenshots and user guide:

1. Writing an Add-on
2. Manage Add-ons

BEAUti 2 needs to be updated first, before these 2 pages can be re-written.

Walter

Additional comments from GC issue

Sep 13, 2013
Project Member #1 alexei.drummond

I prefer "Package" to "Plugin". Package sounds like something you could write a paper about and be proud of (as with an R package).

Once we decide on the right name, it should be applied everywhere, not piecemeal.

Sep 22, 2013
Project Member #2 alexei.drummond

(No comment was entered for this change.)

[rbouckaert]

This seems a goot time to rename the AddOnManager to PackageManager for the v2.5.0 release.

[rbouckaert]

BEAST_ADDON_PATH is deprecated and you need to use BEAST_PACKAGE_PATH instead (though for a time both are recognised) in either environment variables or java properties.

In version.xml files for packages, the element addonapp should be replaced by packageapp, though the former will be recognised as long as there is no element of the latter (for now).

[rbouckaert]

By ba18dcf