answer to you question about way to call external tools: no problem - from eclispe you can anything: external program, batch file etc. moreover, if you use custom build generator - you could use it transparent with eclipse.
i don't think i would switch from visual studio to eclipse in hopes of getting a better ide. typically an embedded manufacturer makes plugins and toolchains that work specificially with eclispe, that's what makes it worth using in the embedded world. for example with the netburner plug-ins, when creating a new project you can just select new netburner device excecutable, or new netburner library, all the default includes and libraries get set up for you and the proper cross platform tool chain is set up for you automatically. in the netburner case it also uses the eclipse managed build process (as opposed to make files) which i find nice. there is also support for using make files if you prefer that option.
while i have a couple of tools set up to run as external tools (lint, an auto version updater, dos prompt etc) most steps can be triggered from pre-build or post-build steps or there are many many add-ons for common needs like source code management, bug tracking, etc. there is great support for svn, trac and mylyn for example. i use both vs2010 and eclipse. i like them both but vs2010 is the better ide. it's a little hard to compare because i do c# (and a little c++/cli )in vs and c++ in eclipse. that said, i wouldn't relish the though of trying set up vs to do my embedded tasks.
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