Fix for bug 53856: "Option reference not reporting built-in includes paths to scanner". Changed the constructor for the OptionReference so it only creates a list if it finds built-in path or symbol definitions in the manifest or project file. The getter method for built-ins also concatenates the definitions it contains with those of its parent.
Undid the changes to the geenrated makefile builder since bug 53253 has been corrected.
Fix for bug 53861: "Cannot reset tool command back to default". Changed the way the configuration sets the tool command when the value is the same as the default.
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