The following is the directory structure I use for organizing my files for work and projects, and life.
inbox/
notes/
|
|--inbox.md
|--todo.txt
`--done.txt
projects/
|
|--project_1
`--project_2
notes/
|
|
|--done.txt
|--home_project_1_note.md
|--work_project_2_note.md
|--inbox.md
|--todo.txt
archive/
|
`--YYYY/
|
|--notes/
| |--home_project_3_note.md
| `--work_project_4_note.md
|
`--projects/
|--project_3
`--project_4 ...