I am running Ubuntu 15.10 with Eclipse Mars 4.5.2 (from the Oomph installer) and and Java 1.8 and Python 2.7. I am attempting to the PyDev 5.2.0 plugin for Eclipse. Installing with Eclipse's update manager seemed to go okay. The only problem is that I can only see PyDev related options when I run Eclipse with sudo.
-clean option.The first two didn't allow me access to the PyDev options in Eclipse. Running as a normal user with the -clean option did let me see the PyDev options, but running as a normal user without -clean made the PyDev menu options invisible again.
Finally, I noticed that running Eclipse as root made the PyDev options appear again. This suggested that there was some ownership or permission problem. Since my Eclipse installation and plugins are in my home directory, I made sure my user has ownership over everything in the home directory. I also reviewed the permissions of files related to the PyDev plugin, and it appears I have the appropriate permissions, but since I do not know which permissions each file ought to have, I am not sure.
I am not sure what is going on. It is especially surprising given that I was able to install the CDT plugin not long ago without any hassle. It's also possible the problem might be related to how root's environment is configured compared to my user's, but being able to access PyDev when running with -clean seems to vanquish that theory.
I could just run Eclipse as root from now on, which isn't that big of a deal. However, it is quite annoying not knowing why this is happening, making me feel like I don't have control over Ubuntu and Eclipse.
In my case, upgrading to Ubuntu 16.04 solved my problem. After the upgrade, PyDev was working normally in Eclipse.