I've come to realize that flexibility is very near the top of the list for me as well, to the point that a pay increase would have to be pretty large for me to give up flexibility.
To Do lists:
emacs org-mode and agenda. I have one 'todo.org' file with top-level headings for each project. I keep an org-agenda buffer open to display the todo's scheduled for the current day. I try to go through my todo file once a week and clean it up, archiving 'DONE' items and deleting items that are no longer relevant or haven't been touched in a while. All my emacs org files are synced via dropbox. BTW, org mode really is amazing. I keep finding little nuggets that delight when reading about others' org-mode setups.
Bookmarks:
Pinboard, as well as pocket/instapaper for offline reading of bookmarks.
Financial tools:
Mint by intuit to keep track of all my accounts, numbers/excel for budgeting.
Calendar/Reminders: Google calendar and macOS calendar. I use siri/google assistant to capture spur-of-the-moment things that I don't want to forget.
Files on Disk:
Dropbox. Backblaze for backups. Google photos and icloud photos for extra photo backups.
Wikis/General Notes:
Emacs org mode. I keep a journal.org file, that I sporadically update, as well as an ideas.org file for things I'd like to investigate/try build in the future.
I use evernote for lists/notes from mobile devices as I haven't figured out a good way to use org files on iPhone/Android.
There isn't much overall integration, I just know that for important files I reference dropbox, Financials and Bookmarks have their own services, and then notes are going to be in emacs or evernote. Events/reminders handle themselves as I typically schedule them in the stock calendar/reminder apps and forget about them until I get a notification. I don't find the lack of integration to be a problem actually, as long as I know where to look for something based on what it is (e.g. notes -> orgmode/evernote, events -> calendar/reminders, files -> dropbox etc.)
Ymmv but I sync my notes files via Dropbox across several computers. I wrote a simple elisp function that runs on startup and opens my "todo.org" file. The only unsolved piece of the puzzle here for me is mobile: I haven't found a good way to view/edit org files on iOS.
Just finished atlas shrugged. It got a little long, but for the 1st 80% of it I was pretty engrossed by the plot line, themes and all aside. I enjoyed it
I've run into problems with large-ish files in git repos, binaries accidentally committed etc. I'm genuinely curious, is there a good way to use git for the size repositories that you mention?
I'm with you on the coding comment especially when non-coding people use it to describe programming/coding as a menial, mindless task. I've also had the same thought that maybe I just want my job to sound cooler...
Your concerns about quickly flipping through pages are valid. I regularly read programming books in ebook form, mostly since they are cheaper, but it isn't a perfect experience. I tend to get used to searching and setting a lot of bookmarks. One other note: Charts, graphs and tables tend to not translate well to a smaller screen (I have a nook simple touch, YMMV)