The game is great, but some things could be improved.
1. Clippy's health: It's too high compared to the damage that the "red folder" and bosses do, making it almost impossible to die in a normal gameplay. Maybe less health/more damage could solve this OR you could add difficulty options that would give the player less health and/or more damage.
2. Non-existent cooldowns that the skills/powers have: the game is easily beatable by just spamming "shift" or "control" every time that an enemy appears (after you got the skill/power). A 2-5 second cooldown would be great just to stop this kind of action + give the player a little more of a hassle avoiding projectiles.
3. Keys: they are easily collectable by just running and going back (because the enemies don't do much damage), making them kind of useless. You could add more damage to the enemies (already suggested) or make the key only appear after you killed every single enemy on the room/folder.
These are the main ones that I could think of right now. I hade some ideas that could be developed, but that's to you: making the keys spawn at random spots/folders instead of the same ones every run and making the enemies spawn at different locations every run (since it's very easy to beat the game in 2-4 minutes when you remember the folders/locations).