TagSpaces is a cross-platform, privacy-aware file manager and browser that has some note-taking capabilities. It allows you to organize your files and folders using tags and colors. You can download it for Windows, macOS Linux and Android.
The TagSpaces Web Clipper allows you to collect web pages, bookmarks and geo-coordinates as well as screenshots from the Web.
The built-in Markdown editor allows you to create notes that include tables, math formulas, todo lists and diagrams. TagSpaces can be connected to any folder on your hard disk and allow you to quickly browse its contents. You can add labels also known as tags to any folder or file. In the Pro version, you can also add descriptions and geotags to files and folders. Geo-tagged files or photos can be placed on a digital map. In the Pro version you can also turn every folder into a Kanban board, which allows you to represent process with the help of cards(files) and columns(folders). Cross-references can be achieved by using tags in the folder hierarchy. You can search for files using any combination of tags with the built-in search.
TagSpaces can also browse files placed on S3 compatible object storage like from Wasabi or AWS S3.