the fore with the rise of Java, where the class name must be the same as the name of the file in the file system (possibly a questionable design decision, but one we now have to live with).
Some IDEs, starting with IntelliJ and now including Eclipse and others, offer a number of refactorings from within the IDE, including the renaming of classes. This can result in a number of changes throughout the application where that class is explicitly referenced in other classes - all handled by the IDE, including automatic checkouts and renames in the underlying SCM tool if that tool's plug-in supports it.
Handling renames across branches is one of those areas where there are different levels of SCM tool support - make sure you are using one that supports it well - or at least well enough.
The problem becomes worse if you have serious parallel development going on. If 3.5 is your base release and you have two major enhancements A & B in development. The business doesn't know if A will turn into 3.6 and B into 3.7, or the other way around. Or perhaps both will merge together into 3.6. Until the modules (which share a common database and rely on some common classes) are close to complete and have a release cycle planned concretely it's hard to refactor any of the base classes because then you make dependencies about them both being released together, or one before the other.
Note that the results of this type of requirement and the associated overheads need to be made visible to management. They often don't realize directly the maintenance overhead associated with being able to do this, and can blithely agree to client requests without considering the consequences (and that perhaps the client should either be paying more for the requested flexibility, or indeed that less flexibility should be allowed).
And yet in spite of this, we have all personally experienced many projects which have been doing refactoring in parallel development projects for more than a decade, and this would not have been possible without branching (and good tool support and knowledge of how to use those tools). Using strict code ownership and file-locking would have made things too unbearably slow to be productive. With sound parallel development practices that group together modifications made toward the same purpose as logical (rather than physical) units of change, the projects had little or no hassle and no waiting around for other folks to check something back in to release a file-lock.
This highlights the fact that the most successful parallel development shops don't do parallelism at the granularity of single files or classes/methods. They do it at the level of projects and subprojects and tasks. If you do it at the file/class level granularity it becomes too complex track. If you do it at the project/task granularity it all fits into a single change-flow hierarchy. The "Streamed Lines" paper is clear about the requirement for project-oriented versus file-oriented locking. Otherwise it looks as if all those practices are referring to individual files and it seems crazy.
This also raises the need for a version control tool that can not only do branching, but that lets you use symbolic names for branches (not just revisions on the branch, but for the branch itself). If the tool tracks both divergence (branch-points) and convergence (merge-points) then merging is no longer the nightmare that everyone always assumes it must be. In fact it's often quite trivial. And some of the more modern tools even provide some automated and intelligent merging support to make