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It's interesting to see people actually use ATOM on Linux. I've heard about it as I had a Mac user trying to convince me to use it a while back (face to face convince attempts none the less!).
Regarding Geany and project management, in general it is able to do this quite well in my experience. You can open multiple instances of Geany at any given time and thus have multiple projects open and you can use the "Projects > Recent Projects" to quickly switch between projects.
In addition Geany will automatically load up your last used/edited project when you open it (at least it does for me!)
If like me you also use a private git repository you can also configure the Geany git-changelog plugin which will highlight changed, removed or added lines which can be super helpful when editing files (That: Did I change this line? moment).
Now, for uploading to test servers or live servers there is indeed no plugin for this. But you can cheat ;).
You can have a "terminal" open inside geany, and you can have it displayed right below your editor, and this basically means you have a fully fledged terminal inside your IDE for running scripts or otherwise, personally I use the terminal to run a lua script which is able to perform several tasks for me including uploading the files to a remote server.
Here's a screenshot of my IDE setup with a mini-php file and in the test file you can see the mini-app I have running in terminal and the git change bar highlighting an added line and a changed line :).
http://imgur.com/vTpFZCN
(My mini-app uses SSH to upload files using SSH keys.)
One thing I will say though: Keep a proper file manager like pcmanfm handy when using geany, sometimes geany can be a bit lacking when it comes to filesystem management, it does have the basics though but sometimes I feel I need more.
Also another negative compared to Eclipse which I used to use is lack of a proper git plugin, I mean the current plugin works for displaying changes and that works great, but it cannot be used to view the git tree, make new commits etc. You'll have to use git manually for all of that.. or an external application like "Git Cola" if you can't use the cli version.
All of this of course is subjective to a users actual needs but this is more detail on why I prefer geany as it quite literally does all I need it to do when dealing with my php, html, css, js, lua, python scripts :-).
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* Eclipse for Java
* ViM for Rust or C/C++
* Atom for Rust and C/C++
* Gnome Builder (or Gedit) for Rust and C/C++
Depends on my mood. Sometimes I find ViM to be a hell of a lot faster for editing. But if I need a good overview of a project it's not very suitable, that's when I start using Atom or Gnome Builder.
Atom with a ViM style plugin is good too. Actually, any editor that supports a proper GUI and ViM mode is good in my books.
Used to use Komodo IDE for Python, PHP, basically any web stuff. It's a nice IDE, but I no-longer do web related stuff. And I've pretty much junked Python and write any quick script stuff in Rust now.
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You might like Komodo Edit? (Komodo IDE is the paid version, cheap and damn good). Gnome Builder is another, but may not be suitable, it's more specialised towards Gnome.
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