My issue isn't strict, I don't know why everyone says that. I have a small sample program that works perfectly, but I'm trying to merge something like it into the main code I'm working on. I think my problem is in the hd::store=; statement. When I push things into another array, does it push the values or just a reference to the values? Can I make it push just the values?
Perl arrays store scalar values. Scalar values are things like numbers, strings and references. When you copy an array (which includes push, pop and so on) you copy the scalar values of the elements. In a sense Perl doesn't do multiply dimensioned arrays. Instead it allows you to have an array of references to other (lets call them 'owned') arrays. When you copy an array of arrays you only copy the references so you end up with two arrays containing references to the same collection 'owned' arrays.
You need to provide a way to make a deep copy of the data. Data::Deep may help (I've not used it). It may also be worth looking at PDL which is designed for data manipulation in Perl.
BTW, I strongly endorse the other comments relating to using 'my' and package variables. Most likely if stuff broke when you used 'my' strict was highlighting either a bug or a design problem in your code.
Perl is the programming world's equivalent of English
Global data is, IMHO, always problematic. If you are looking for up-to-date on-line general introductory tutorials, I would suggest perlintro, perhaps followed by chromatic's freely downloadable Modern Perl.
Oh, if you mean why do I define all my variables with packages like main? Because when I first started perl, whenever I tried to use "my" my program wouldn't work. So I just started giving things packages, and haven't stopped. It just seems more stable.
... when I first started perl, whenever I tried to use "my" my program wouldn't work.
It would have been very useful to have explored the reasons why your use of lexical variables wouldn't work. It's not too late to begin!
... packages ... just [seem] more stable.
Package data is global data. Global data is, IMHO, always problematic.
The story goes that during one of the Pearl Harbor attacks on December 7, 1941, General Walter Short, commander of the Army forces in Pearl, was struck in the chest by a spent 50-caliber machinegun round and knocked to the ground. The bullet's impact didn't even break the skin, but when someone picked it up and showed it to Short, he said "It would have been better if it had killed me."
When the day comes (and come it will if it has not already) that you are knocked on your ass by a chunk of global data at the end of a long trajectory from its point of origin, you may have some of the same feelings.