I write notes in a single plain text file, using the dates they are made to cite them in newer notes. There are two types of notes, brainstorming throw-away ones that maintain the process of thinking about a problem or of learning something (such as carefully reading a paper), and more lucid ones, with some re-reading value, which are marked differently and have a one-sentence summary. The notes are intended to never be made public, so that I feel free to use them to resolve any silly confusions.
I write notes in a single plain text file, using the dates they are made to cite them in newer notes. There are two types of notes, brainstorming throw-away ones that maintain the process of thinking about a problem or of learning something (such as carefully reading a paper), and more lucid ones, with some re-reading value, which are marked differently and have a one-sentence summary. The notes are intended to never be made public, so that I feel free to use them to resolve any silly confusions.