We can encrypt only part of file tree, for example encrypt /user/notes/secrets/* and don’t touch /user/articles/*. So until you decided to read/change your secret notes you don’t need to enter password.
It’s also possible to ask for passwords only for some files with specific extensions, for example /user/notes/ids.gpg.
All major browsers vendors work on implementing WebCrypto standard now. It will provide to Javascript access to first-class random generator and basic cryptography methods. In the meantime we can use a WebCrypto polyfill.