Ask HN Researchers: What do you use for organizing your notes?

Right now I use simple latex and text files and let OS and Dropbox help me organize these scattered Notes ; but is there a good layer that would let me organize them?

Features that I would like:

1. Tag Notes and not deal with categories (folders and subfolder).

2. Search Notes and within the notes.

3. Back up the entire library of notes that I have taken.

4. Batch Rename notes.

5. Sort the notes of certain tags in preferred order. I hate renaming files starting with numbers(1.File 2. File) to force order in the file system.

5. If there were an abstraction of Workspace that would be awesome. So that I could save my session or revert to a previous state of notes. Or I could share a particular snapshot of my research notes. But not really necessary.

Almost like the Lightroom for my research documents. I wouldn't mind using an inbuilt text editor.