“A place for everything, everything in its place.”
As Benjamin Franklin pointed out there are two parts to organization. The first is that absolute everything needs to fit somewhere. With software this really translates to having a solid 'reason' for every little bit in the system, be it config files, methods, data etc. and a reason for its location. It all needs its place, and often for that it also needs some level of categorization. "It doesn't matter" is synonymous with "it's not organized".
This includes names, conventions, even coding styles. Everything. Each tiny piece of work, each little change should all have its place. It should all have a reason for being where it is, as it is.
The second half of the quote is just as important. What's the point of having an organizational scheme if its not being used. As new things are added, they need to be added into their place. Sometimes it’s clear where they belong, but often times it hasn't been explicitly documented. Assuming that lack of documentation equates to lack of organization (and as such it is a free for all) is a common failing amongst inexperienced coders. Things can be organized with having an accompanying manual.
Failing to keep a development project organized is the beginning of the end. Disorganization is probably the worst aspect of technical debt because it is a direct path into various forms of spaghetti. And spaghetti is a quagmire for time, either to fix bugs or to extend out the functionality.
Part of software development culture over the last couple of decades has been a strong desire for 'freedom'. Freedom is great, but used improperly it just becomes an excuse for creating disorganization. For instance, utilizing the full freedom to create a new screen in a much fancier way than the existing ones is really just breaking the organization of what is already there. It's like helping someone dry the dishes in their kitchen, but then insisting on placing the clean stuff in any other location than where it actually belongs. It isn't really helpful is it?
It's true that in some regards a well-organized existing development project is a boring one. If the work isn't exceeding the existing organizational bounds then it can really just fit in like all the other pieces. But success in development doesn't come from making any one small piece of the system great, it's an all or nothing deal. The system is only as good as its crappiest screen or stupidest functionality. Thus changes to enhance it or its organization can't be selective. The whole thing needs to be fixed or it’s actually just making it worse.
If you're evaluating an existing development project, disorganization is easily the best indicator of the future. A small project can get away with disorganization, but anything larger absolutely needs organization to survive. If it is lacking or failing, then the whole effort is in deep trouble.