Hi,
For modifying classpath.txt and librarypath.txt one needs write acces to the toolbox\local folder.
Note that for 13a and newer one can create a javaclasspath.txt and place it anywhere on the MATLAB search path. This file is picked up by MATLAB at startup and merged with the shipped classpath.txt then. So for 13a and newer one does not need write access to the classpath.txt. However for the librarypath.txt one still needs write permissions.
For example modifying this files is often needed when using DATABASE Toolbox in order to install a JDBC driver for MATLAB and allow the usage of windows authentication.
This needs to be done once, so the IT can take care of it.
For a user who works with MATLABs static java classpath and in an older release as R2013a write access is 100% needed. For newer releases he can work with the javaclasspath.txt and will be fine.