Jot
Jot is a tool that helps you take notes in your terminal without leaving files lying around in your project's directory. It does this by grouping all your notes (a.k.a. jots) under a "tracked" workspace. Your "jots" are actually stored in an sqlite db and can be viewed inside directories that they were created in using jot's commands. All jots are opened in the default editor (you can change it using update-alternatives)
Usage
Jot - jot stuff down without messing up your workspace!
usage: jot [file] edit jot file in working directory
or: jot <command> [<args>] perform misc operations
commands:
-t Track current directory
-u Untrack current directory. Note: this will delete all jots in the dir
-l List jot files in the working directory
-o Print file contents on the standard output
-d Delete a jot from the working directory
-m Import a file. The resulting file's name will be the jot's name
-clean-all Remove all jot files in the system (dangerous)
-list-tracked List all tracked dirs
-help Print Help (this message) and exit
Install
You can download a binary (for linux) from here (don't forget to mark it as 'executable').