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I’d say do whatever you need to do to become comfortable organizing your code into multiple files. In the long run you’ll be happier with short files that contain all the code—and only the code—that addresses a particular concern. I would consider a 1000 line file to be exceptionally large and probably in need of refactoring.
I think you’re right that BBEdit’s projects feature can help here. Other features that may be able to help are:
File > Open File by Name… - Select the name of a file and hit ⌘D to open that file.
Search > Multi-File Search… - Search all open files, all files in a project, all files in a folder, etc. Filter by file name, type, etc.
Hope you find this useful!
-sam
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