Debian – uninstalling iceweasel with apt-get autoremove

APT maintains an indicator for each package, telling it whether the package is manually installed (installed because the user/administrator wanted it) or automatically installed (installed only because it's a dependency of some other package). That's what apt-get autoremove uses to determine what to remove: it removes packages that are marked as automatically installed, but that no currently installed package requires.

You need to mark the gnome package, or whatever Gnome package corresponds to the bits you want to keep, as manually installed. It's easiest to do this in an interactive tool with access to the automatically-installed setting:

• On the command line, call aptitude unmarkauto PACKAGENAME to mark PACKAGENAME as manually installed, or markauto to mark it as automatically installed.
• In Aptitude, move to the line corresponding to a package, then press m to mark it as manually installed, or M to mark it as automatically installed.
• In Synaptic, move to the line corresponding to a package, then toggle “Automatically installed” in the “Package” menu.

Note that (at least as of squeeze, I haven't checked wheezy) gnome-desktop-environment depends on all of the official Gnome components, including empathy. I suspect you had gnome-desktop-environment installed, and removing the empathy package had to remove it because of the dependency. If this is the case you should now reinstall gnome-desktop-environment. (If you don't remember, you can find a history of what APT-based package managers did in /var/log/apt.)

Instead of purging and installing empathy, you could have just done apt-get -t wheezy empathy to install the wheezy version.

About your requirements, Iceweasel is the supported Firefox derivative (fork), I'm currently running debian as my desktop OS at work and use iceweasel every day, no problem. Gnome3, I think it'll be available on the next stable release, BTW what release are you running? Squeeze? If so I think (IIRC) Wheezy will have it. And finally, about graphics performance/quality, that depends a lot on your graphics card and its driver, but if you think of it like having transparencies, windows closing with fancy effects and so on, you'll need a moderm desktop or compiz (work with gnome2) which I think its available on stable (wheeze).

I have modified a bit your sources.list for wheeze, do you mind to test it and report back?

deb http://http.us.debian.org/debian/ squeeze contrib non-free main
deb-src http://http.us.debian.org/debian/ squeeze main

deb http://security.debian.org/ squeeze/updates main non-free contrib
deb-src http://http.us.debian.org/debian/ squeeze/updates main

# squeeze-updates, previously known as 'volatile'
deb http://mirror.cse.iitk.ac.in/debian/ squeeze-updates main non-free contrib
deb-src http://mirror.cse.iitk.ac.in/debian/ squeeze-updates main non-free contrib

# 3rd party repositories
deb http://packages.dotdeb.org squeeze all
deb-src http://packages.dotdeb.org squeeze all
deb http://www.deb-multimedia.org squeeze main non-free

If you happen to be using wheezy or sid you'll have to change all squeeze ocurrences for the one you're using.

Please, backup your sources.list before replacing it, then test it as follows:

Refresh caches

# apt-get update

Search package

# apt-cache vlc

Install package

# apt-get install <package_name>

If find trouble, please report back with output for those three commands, or at least for the first and last.

Also, if you are already using Wheezy or sid, forget what I said about Gnome3 not being available, it should be there but wheezy is yet to be release and sid is always the development branch.