Eclipse CDT organize includes but don't add new ones - eclipse

In Eclipse CDT I can organize my includes with several options as explained here. When I do this, it includes some system libraries that I don't want. I would like to use this to put the includes that I've written in the correct order and to remove the ones I'm not using, but I don't want new ones being added automatically. Is there an option for that, I couldn't find this.

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Extend or configure Eclipse compare files functionality

Eclipse has built in functionality for comparing files, but how can I configure that functionality? Say I create a new file type and want an external program do perform the diff. How do I set that up?
Can I create an Eclipse plugin to add my own plugin for handling file comparisons? Or perhaps that is the answer to the first question...
You may want to look at the EMF Compare Project which helps build compare editors for EMF models. If you don't have an EMF model for your file type, you can either create one or look through the source code of EMF Compare to see how it works.
The developer guide explains how to use the code to write your custom viewers.
There is a plugin integrating Beyond Compare into Eclipse. As it is open source, you might get a clue by looking at its sources.

Eclipse plugin to colorize/visually flag entries in the Package Explorer?

I am looking for a way to colorize entries in Eclipse' Package Explorer:
In bigger projects you have dozens of files in a package all listed underneath each other. This makes it hard to find the file you look for (e.g. for right-click operations). So it would be nice if I could manually colorize some entries.
Does a plugin for this exist?
This is one that I was using before. It lets you set rules and tints icons accordingly:
Label Decorator
One way to have Eclipse filter the classes you see is to use Eclipse Mylyn. You create tasks that you work on and Mylyn will remember the packages and classes associated with a certain task. It will then filter out all other classes/packages. This gives you an editor that only shows the information relevant to a specific task.
I suggested Mylyn for a different problem aswell and in that answer I gave a bit more information.

To modify a core eclipse plugin

In order to modify an eclipse plugin, what are the steps to find its editable code ?
I read and debug source provided with eclipse distribution but to try a fix in org.eclipse.jdt.internal.corext.codemanipulation behavior I need to make it editable.
Well, the source repository is available at eclipse.org, the plugin compiled with the source should be available from the standard eclipse update site.
I'm guessing you are considering changing the source, recompiling and using your plugin instead of the standard one? There is a different way to change functionality, its with fragments. For example, look at a question I asked earlier, follow the links in my text and Andrews answer for more information.

Programmatically make use of eclipse's merge and diff viewers

When a text conflict occurs in Bazaar (and many other dvcs) a .BASE, .THIS and .OTHER file is produced. Its then up to the user to make use of an 3 way merge tool to merge the conflict and then mark it as resolved.
I would like to get hold of all the registered merge viewers in eclipse and give the user an option to merge the conflict with any one of these. (with the TextMergeViewer being an default option). I suspect that I would need to some how programmatically provide the 3 files to these mergeviewers and maybe write some custom code to wrap the BASE, THIS and OTHER files to tell the merge viewer where the differences are. (interpret the "herringbone" markers like <<<<<<<. etc)
Not exactly an answer, but at least some starting points:
You could try looking into the code of the current Compare Viewer using the Plug-in Spy (directly available with eclipse3.5)
(source: eclipse.org)
(ALT+SHIFT+F1)
Most of the eclipse sources are also available here.
The org.eclipse.compare.CompareUI is a start, for example.
Once you have a basic understanding of how the Compare mechanism works as a plugin, you can write an fragment (also illustrated here) to extend the current compare plugin.

Grouping Files in Project Explorer in Eclipse

I am newbie to Eclipse, I am planning to use it for AVR development with WinAVR and gcc.
The feature I am looking for is the grouping of different files in the project, like all headers together, all source files together and all files excluded from the build together etc.
I tried AVR Studio from Atmel, it has this grouping feature but it lacks several other features which Eclipse supports. Any help to configure Eclipse Project explorer to display the project files in this way would be appreciated and helpful for me to decide the IDE to use.
Note: I know that I can manually add different folders for each of these groups and move the files, but that moves the physical files, and breaks the relative path in the code, and other comilers/IDE's. I am looking for logical grouping of files.
Unfortunately there is no general way for a user to configure the grouping in the Project Explorer, the grouping is setup based on the code that controls the content (i.e. CDT, JDT, etc). I think it would be interesting to have this feature, but it's not clear the UI that can be used to specify it. You are welcome to submit an enhancement request to add this to the Eclipse Platform UI project. And giving an example of how it's done in another product would be helpful.
Thanks Francis, looking at your profile I think I found the right person to solve my issue :)
I have opened it as a bug (as I could not find a feature request in bugzila) Bug 296514 - Logical Grouping Files in Project Explorer in Eclipse
I have attcahed screenshots of both AVR Studio and Eclipse project explorer. That should give you an idea of what kind of UI features I am requesting. I can difinetely provide more information if you want.
I think what you are looking for can be done with Working Sets.