There are some improvements regarding speed especially for systems with expensive file i/o or calls to executables:

• option DOT_DRY_RUN does not call dot from doxygen. Generation of files can be done afterwards e.g. using xargs dot.exe.
• there's a look-up table that checks if the dot-graph has been already written to a file. This avoids file i/o checking if the file already exists.
• the dot-files do not start with getOutputFileBase(). This reduces the number of files with identical content and also the time to render the graphs.
• there's a look-up table that checks if the uml-graph has been already processed. If yes, it is skipped.
• PlantUML file inline_umlgraph_* is now split up into multiple files. PlantUML supports only multi-threading for separated files. Thus, writing all graphs to one file uses only one thread in plantuml.
• The inline_umlgraph files contain now a reference to the origin. This helps to fix syntax issues in the graphs.
• Plantuml syntax errors are now reported as warnings.

This is my first pull request, so consider it as a draft proposal far away from been perfect and fully tested.