I will add Total Commander (for Android). While not FOSS (AFAIK), it is freeware, features dual panels and also supports SFTP/SMB/CIFS for copying from/to a NAS.

https://www.ghisler.com/android.htm

https://www.ghisler.com/tcandroid3.apk

https://www.totalcommander.ch/android/plugins.htm

Horoable mentions: https://kdeconnect.kde.org/

https://localsend.org/

And of course install everything with: https://github.com/ImranR98/Obtainium

I'm a big fan of Material Files for managing on the phone directly.

So part of the problem is storage is a mix of standardized folders (download, etc), custom app folders, and stuff created by the user.

It's a mess because apps don't always use system defined folders.

Another issue is the protocol for connecting via USB is pretty weak - it was never intended for real file management.

My approach has been to sync my user partition (all the folders you see with a file browser on the phone) to a home PC and manage files there.

This gives me an easier interface to use and simultaneously provides a backup to home.

You can either Resilio Sync or Syncthing - Resilio is a little easier for someone new to sync tools, and unlike Syncthing it can have a single folder pair set to the root of your user partition.

I use both for different tasks - for your setup I'd install Resilio on your phone and PC, setup a folder pair that on the phone points to the root of your user partition, and on PC pick a folder that's only used for phone data.

Configure it to only use wifi (which I think is default anyway) and also only run when plugged in. The initial sync job will be heavy and take some time, so you don't want to kill your battery. You can change this setting later.

Now whenever you're on WiFi and charging, it'll sync any new files/changes back to your PC, and the best part, any changes you make on the PC will sync back to the phone!

For example, the download folder is always a mess, so I manage it at my pc - deleting old downloads, moving memes from download to another folder etc.

Another great advantage here is all your photos will sync to your PC so you have them in 2 places. They're a lot easier to sift through, re-organize, rename, tag, etc, on the PC using your favorite tools. Then all those changes sync back to your phone next time it's on wifi and power.

Just ignore the folders that start with a dot - those are app data folders, often temp files. They get changed and recreated all the time, so doing anything with them is a waste of effort, and may cause problems.

Edit: For file management on the phone I use both SD Maid and Mixplorer.

The flexibility with Mix is impressive, and it easily/quickly connects with network shares of all types.

What's the exact problem, and what's your goal? If you just have a bunch of junk you don't care about, the best option is to just wipe it.

I use this thing https://f-droid.org/packages/eu.darken.sdmse/

There are a lot of apps, such as Material Files, which will show your file structure. Depending on your desired outcome, there are also apps that will help you organize the files.