Organizing Notes

https://unsplash.com/photos/5bYxXawHOQg
Requirements
Data should be easily updatable (this is the input) & easily accessible (this is the output). Currently, my notes are stored on a GitHub repo. That means:
Easily Accessible
This can be broken into 2 scenarios, depending on sensitivity of data.
Insensible notes should be searchable online
To have them easily accessible, I want them to be full-text-indexed and searchable.
I want the insensitive data to be searchable online, so that I can have access to my notes without access to my computers.
Existing solutions: Are there any? What are they? How good are they?
GitBook (Figure 1)
pros:
Has URL form -- e.g. https://tslmy.gitbook.io/k/?q=typora would give you search results in my Wiki with the keyword "typora".
cons:
Search is dynamically loaded -- slow to render.
An online service -- does not work offline.
GitHub (Figure 2)
pros:
Has URL form -- e.g. https://github.com/tslmy/know/search?q=typora&unscoped_q=typora would give you search results in my Wiki with the keyword "typora".
Statistically loaded -- renders faster than GitBook.
cons:
An online service -- does not work offline.
Figure 1: Search UI on GitBook
Figure 2: Search UI on GitHub
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Sensitive data to be kept offline and still searchable
Existing solutions: Are there any? What are they? How good are they?
OneNote / EverNote / Notability
pros
robust functionalities
cons
walled gardens
macOS Spotlight
pros
really easy access -- integrated with the OS
cons
does not support notes in walled gardens (not even Zotero references)
not portable -- different OSes offer incoherent experiences. This actually resembles the "walled garden" critique from the previous option.
command-line tools
resources
features comparison of several CLI regexp search tools: here​
speed comparison of ~~~~: here​
Looks like the best choice is ripgrep . 
Need to do:
auto-exporting data from all sources to plain text and save locally.
pros
cons
Easily Updatable
The best option for now I've found is GitBook. It's got a decent webUI editor (although it has a list of quirks -- see below -- and is slow on an old computer), syncs to your GitHub, and its syntax is interoperable with Markdown.
List of quirks of GitBook:
aggressive undoing
when you copy something from a list and paste it somewhere else, the whole list indention builds up again. e.g., if you copied some text from a 3rd-level nested list and past it on a 2nd, you will get a 5th-level result.
TODO: This section needs expansion.
Solutions
Stick with GitBook for adding & updating public notes. TODO:
Find a way to auto-update local copy of GitBook notes.
Validate that I can conveniently search locally all my notes (that means private notes as local md files + public notes from GitBook) with ripgrep. 
Add a custom search engine to my Chrome that searches the GitHub repo directly.
(Deprecated) How Notes & Writings Can Be Categorized
Classifications of my writings & notes, and where to put them.
Type
Updatable?
How Refined?
Can Made Public?
How valuable to others?
Diary
Never
-2
N
0
Personal Journal
Daily
-3
N
0
Credentials / Passwords
At times
N/A
N
3
Academic papers
Never
3
Y
3
Various Essays
Never
2
Y
2
Quick Notes
Seldom
-1
N
1
Reviews / Summaries
Maybe
1
Y
2
Web Clippings
Never
N/A
N/A
1
Translations / Transcripts
Never
3
Y
2
N/A means "not my own work, thus does not apply."
Numbers are on a 7-point scale.
How I Allocate Apps to Different Note-taking Purposes
Crossed-outs are what I used to use but moved away from (due to death of product, etc.).
Note-taking and Storage
Course notes / meeting notes that better be hand-drawn: Notability (iPad)
Diary, personal journal: Day One OneNote
Course reviews and summaries: Evernote Notability, course-specific folders, and -- in cases that the notes may be shared -- my academic website. 
Scribbles, jots, etc.: A folder full of plain text/markdown files.
Synced with Simplenote Dropbox.
Read with Notational Velocity, nvALT fsNotes.
Editors and Word Processors
Coding/writing temporarily - Sublime Text
Quickly generating PDFs from Markdown - Mou Typora
Academic writing (essay, things with a formula/equation, etc.) - LyX
For language-checking - Hemingway Editor + SlickWrite
Mind-mapping - MindNode 
(Math stuff excluded)
(Office suites excluded)
(Reminder and Calendar excluded)
(Rare-format editors excluded)
Cloud Storages
Mobile Syncing - Dropbox
Google Office - Google Drive
Microsoft Office - OneDrive
Backup - Box