Auto update must become OS-aware
This means that on Linux auto update is entirely apt-get based (or whatever mechanism the distro has).
On OSX we might use something like Sparkle.
The NetBeans specific auto update implementation should be just a fallback plan. Having it use BitTorrent too would be nice (see my experiment regarding this).
The custom notification mechanism and popup should be replaced by the OS notification, if available. This means using Growl on OSX and whatever Ubuntu has nowadays.
Git support should be part of the official release: help these guys make it happen!
Mercurial Queues and 3 way diff would also be a nice thing.
Btrace should be bundled with NetBeans and integrated with the existing debugger and profiler. I want to either use the manual debugger/profiler, run normal BTrace scripts or control the debugger or profiler via BTrace scripts! This means a Debugger/Profiler dedicated BTrace API.
Out of process indexing
Indexing takes way too much CPU/memory and should be moved outside the main process (think Google Chrome Multi-process Architecture) since it triggers ugly memory spikes. The design is also kinda broken: preindexing needs almost a full IDE launch during build.
I'll try to expand some of these ideas into dedicated posts.
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