Cannnot build java project in Eclipse: Parent of resource is marked 'read-only'
if changing existing file permissions is not possible, you can also specify the build folder separately (assuming you are able to write your changes into the .project file).
Right-click the project and click properties -> Build path
In there, change the default output folder.
I had the same issue and solved it by granting write access to my workspace folder.
Some hints of how doing that in Linux can be found at: Change read/write access of a folder in Ubuntu Linux