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The python script makes sure to remove duplicates from the deps.make. so the final SVG file looks good even if the dependency list is duplicated two or more times. It would be better to avoid the duplication from happening which at this time I do not know how to fix...
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The python script used to generate the .svg with the dependency tree uses os.system() to run dot. This leaks really very badly, as in, stdout is changed for the entire application (really stupid implementation if you ask me, but there may be some useful needs for such?!) It can be fixed using the popen() function instead.
See: https://stackoverflow.com/questions/21428622/clear-stdout-in-python-cgi-after-os-system