I can't do too much to replicate those in MS Windows since it has it's own convention in doing things. However, some "hack" based on the principle above still useful and makes things easier. Here's what I do :
- Put documentation together in doc dir, especially for libraries. Even when they are installed by default in their own dir, I would copy them under it. This make searching for something like an API doc very convinient, especially in a development that use several libraries at a time.
- Put command-line based tools under bin dir and put this dir on PATH environment variable. It makes PATH variable less cluttered and you have your tools accessible wherever directory you are currently in. I puts tools like ctags, cscopy, sort, custom scripts and sytem hacks here.
- Put libraries outside work source tree, use a dedicated lib dir. Despite their source, how they are used and accessed, I put libraries used in development in one single dir. I find this practice easier for me to just take a glance and in an instant I saw all libraries that I used (or used to used/tried). It's also make the working dir of active code cleaner and give me more clarity. I don't find any urgency to "localize" library within working directory of actively-worked code so far and find this setup to be better.
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