Having my saved web pages as plain files, gives me countless possibilities in terms of portability of my collection... This way I am independent of any online service or product...
A suitable addition to your system for managing notes is the open source tool TagSpaces (https://www.tagspaces.org). With it you can tag, preview and edit your markdown files in one application, without any vendor locking.
You can use the TagSpaces Web Clipper browser extension, which saves parts or whole webpages in simple html files. It is available for Chrome and Firefox from https://www.tagspaces.org/downloads/
For organizing files I can suggest a combination from meaningful folder structure and tags. Mac OS offers a great way to organize files with tags, but it is limited only for the Apple world. There are bunch of tools offering organizing files with tags, but most of them are cloud based or use databases for storing the tagging information. Both ways are locking your files in a third party systems in some way.
A tool for organizing local files and folders with tags lacking these limitations is TagSpaces. If is open source and freely available from https://www.tagspaces.org
This is great idea, but is very Linux/OSX specific, since TagSpaces is multiplatform application, this proposal will not work on Windows or Android platforms.
Other operating systems don't posses the easiness of the tagging system build in OS X. The issue we see in the OS X tags is that they are locked to a particular operating system. Ones you copy/move your files on some other other platforms or the cloud you are mostly loosing the tagging information. BTW, TagSpaces is not only for tagging, we use it for example as a Evernote alternative.
In order to organize files with tagspaces you could use tags, but is not mandatory. You can still relay your local file and folder structure, which is displayed in the application. In a way you can use any conventions with TagSpaces, without a bounding to any file sync cloud service or Evernote.
The contributors have to sign the CLAs only if they want to contribute to the core of the application. BTW, all the tagspaces extensions are licensed under MIT, so here no CLAa are required.
If you place something in the ~/.config it is not portable, ones you copy your files and folders to a usb stick or sync them with dropbox, you loose the meta data.
A simple, open source and file based alternative for Evernote is TagSpaces (https://www.tagspaces.org), with native applications for Windows, OSX and Linux.