Configure Script Processing Bug

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Issue #1524 closed
Steven R. Brandt created an issue

I was working on modifying the java code compiled during the Chemora project, and discovered that a syntax error in the java source file resulted in an infinite number of blank lines being sent to standard output. I traced the problem down to the fact that certain loops in ConfigScriptParser.pl don't check for end of file. The attached patch fixes that, and unifies some replicated code.

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