Dear Friends,
I am uploading my sketches through avrdude. It's very annoying to look for the .hex files in the Temp folder. :0
What can I do so that the .hex files will be created in the same folder where my project is? 
What can I do so that the .hex files will be created in the same folder where my project is?
Re-write the IDE. Enjoy.
PaulS:
Re-write the IDE. Enjoy.
Haha... Good Joke! BTW I'm not gonna do that.
Is there any custom version of IDE which saves the .hex files in the project folder instead of Temp folder?
Have a look at "Wiring", it sort of do what you want.
It puts a folder named "build" in your project folder where all the files in the build, including the .hex-file, is placed.