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When run on a codebase with a large dependency tree the cycle checking can take an enormous amount of time.
In my tests, attempting to make JOM work with ghostscript's makefiles, it can basically take forever (I gave up after 10 minutes).
There is a simple fix for this, implemented here. Once we have cycle checked downwards from a given node, we know that whenever we reach that node again, we need not bother to recheck it as the results will be no different.
Hence whenever we successfully return from the recursive call, set a flag meaning "NoCyclesRootedAtThisNode". Whenever we step into a node, if that flag is set, there is no need to recurse at all.
This is sufficient to make the cycle checking instant for the Ghostscript makefiles.
This does mean that we are left with a 'dirty' tree, in that the NoCyclesRootedAtThisNode flags are left set. I don't think this is an issue, (does Parser:apply ever get called more than once? And if it does, might the tree have changed between calls?) but just in case, I have introduced another pass where we run through the tree clearing the nodes.