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I’m unsure what you mean by “conflicts”. If you have installed WST in addition to MyEclipse you’ll get log messages basically saying that various plugins have already been loaded from another location. This shouldn’t be problematic. However, if you installed some of the WebTools project before installing MyEclipse, you’ll get these redundancies since MyEclipse builds on top of WebTools. We normally recommend installing just the Eclipse SDK, then MyEclipse since we include all the prerequisites at the correct version level to avoid the duplication. More information on that is available in the product release announcement here: http://www.myeclipseide.com/PNphpBB2+file-viewtopic-t-13679.html
The eclipse updater comes up and says there are new versions of thiongs like data tools available, but when I try to install them, it says that this will conflict with myeclipse’s version and make eclipse unstable.
That could be because the “new versions” are milestone builds that need new “milestone builds” of some of the support projects. So, the warning could actually be true in that case.