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What Media Organizer takes in from a drive
A drive holds more than footage: program folders, icons, documents. Media Organizer takes in what matters for your videos, photos and music and leaves the rest where it is. When you add a drive or folder you choose which of its folders come in (how), and you can change it at any time.
What comes in
From the folders you chose, Media Organizer takes in your footage and music wherever they are (videos, camera RAW photos, recorder audio such as WAV, music such as MP3 or FLAC, and photos whose details name a camera or phone), every other file in a folder that holds footage, whatever it is, and camera support files such as a DJI .LRF preview even when its clip is gone. Ordinary images come in only when they sit next to footage.
A camera card is taken in whole, because every file on it matters before you format it, except the files its camera keeps for itself, such as the hidden MISC folder of an Insta360, the PANA_GRP folder of a Panasonic, or the database, thumbnails and proxies of a Sony. Those have no use off the card and the camera writes them again.
Recordings of 0 bytes are left out everywhere, since they hold nothing. To take them in, tick Take in empty (0-byte) recordings on the Advanced page of Settings.
What is always left out
System and junk files (Thumbs.db, desktop.ini, .DS_Store), shortcuts, temporary files and programs stay out, and so do program and developer folders such as Program Files, AppData, node_modules and .git, and any folder holding a software project.
One exception: a copy of a file that is on a camera card is taken in whatever its type, for example a script or a note you keep on the card. A card is taken in whole, so its copies have to be in the library too for the card to show as copied.
Seeing what was left out
After a drive is read, right-click it in the Library and choose Files left out…. The window lists what the last scan left out, by file type and by folder, and the folders that were not read. Show files lists the files behind a line, read from the drive while it is connected, so you can see them before you decide. Include takes a line in from then on. Nothing is left out silently.
Changing your mind
Open Tools > Settings…, choose Drives and click Review… on the drive's row. Untick a folder to take it out of the library, or tick one to bring it in. Files taken out stay on the drive: Media Organizer never deletes them.