gjots2
You can use gjots2 to organize your jottings into a tree structure, adding thoughts and miscellany as you go. You can get it to spit out HTML, XML, postscript, pdf, man, etc if you want (see the online manual for an example of the HTML conversion).
Some people use it for notes, personal bits and pieces, recipes, DocBook XML documents and even PINs and passwords (encrypted with ccrypt(1), openssl(1) or gpg(1)).
It's a bit like the KDE program kjots but it uses the GTK-3 library.
Latest reviews
4
Update: there is a way to work around single file storage. Read manual, find file format (.gjotsfile). Create new file, save it where you want, manually enter filename.gjotsfile. It will be openable from Gjots2, file - open. Still import options could be better, it recognizes TreePad Lite files and imports them, but the whole hierarchy as a single note. So far it's a cleanest Linux replacement for TreePad Lite. I had to find replacement after migrating from Windows, and TreePad for Linux malfunctions on both my computers (Mint 15 and 13, 64-bit and 32-bit). Really like clean interface, functionality and recoverable format of Gjots2.