Regarding the first point, that can be done using any common note-taking software. I use a mix of Evernote and Zotero. I think both are good but each has its us

Regarding the first point, that can be done using any common note-taking software. I use a mix of Evernote and Zotero. I think both are good but each has its use. I tried to use a simple Markdown-based folder structure, but it just was too unwieldy for my tastes.