Can’t help on the dock, I keep in it all the apps I regularly use. but here’s my take on filing system reorganization. I’m in the middle of doing a complete and massive overhaul of my system.
I have a laptop, desktop, iPhone and iPad that all need some set or subset of my digital files.
I have 5 digital “file cabinets” as folders on my main computer. They are labeled Active_Projects, File_Cabinet and then 3, one for each organization where I am a current officer. Within those I have a single layer of folders that sort by name. In my system all someday/maybe folders are kept in my main file cabinet folder, not separate. This is a work in progress so I have many more folders than that right now as I am cleaning up the system. For now as I find stuff related to either organization I just dump the file into that organizations’ top folder and move on as I am focusing on my personal stuff for now.
Within each “file cabinet” folder I have a single layer of folders that sort alphabetically automatically. There are a very few of the folders that actually have a second layer but that is in the minority. Everything goes into a folder, even if it’s just a single file. The digital equivalent of David Allen’s file a single piece of paper.
I have a very few groupings that I manage by naming their respective folders in a way that makes sense. i.e I have folders like Software-Scapple, Software-Omnifocus, Sheep-Breeding, Sheep-Disease_OPP, Sheep-Disease_Scrapie.
I have DEVONThink for small bits of reference and that is undergoing a re-org as well. I do separate the DT stuff into that which I need on the portable devices (iPhone or iPad) and that that I only need on the 2 larger computers. The group names in DEVONThink are the same as the file cabinet and folder names on my main system. One DEVONThink database is an index of my file cabinet folders because I like how I can search in DT better than in Spotlight.
I sync the main and laptop computers with my Active Projects and Reference folders. Association folders only live on the main machine. No folders synch to the iPad or iPhone instead I use DEVONThink to sync items I need on the portable devices.
Use standard filenames with no spaces in the filename so that they are readable on all operating systems.
Use standard file formats that are open source or ubiquitous for my system as much as possible. (ODT, ODS, PNG, TIFF, CSV, SQLITE, JPEG, PDF, ZIP, DMG)
Dated files are in the format --_.
Circa dates use -00- in place of any missing data. Dates that are not circa but to a single level just go that far i.e. 2016_. or 2016-01_.
Range dates use _ between the data ranges i.e 2014-10-05_2015-01-01_.
Hazel rules to automatically file things that come in repeatedly. This is being added to now.
Hope that helps