unable to unstage multiple files and directories from git bash and computer's command prompt - unstage

Question

so my first attempt into web development, one best forgotten methinks in that -when creating my first html file- I was meant to load the saved file using sublime 3 and git gui. I'm unsure how but ended up loading thousands of files - seemingly entire C: Drive -and directories in one go instead of the html file only. Being a complete novice ( clearly so!) I suspect I may have erred in that it was saved on the desktop to start with and not a folder. Please advice how to unstage all these files and directories and get them off git gui and of course crucially my command prompt so I can start the entire excercise afresh . SEE BELOW how it looks. These all sits in the 'Unstaged changes' in git gui I tried git clean and now trying git--rm (attempted removing one file Jedi/ here). If these are the simplest means to remove it please provide how to script the command correctly . alternatively another simple way to remove them, all in one go
Microsoft Windows [Version 10.0.22000.1098]
(c) Microsoft Corporation. All rights reserved.
C:\Users\user>git status
warning: could not open directory 'Application Data/': Permission denied
warning: could not open directory 'Cookies/': Permission denied
warning: could not open directory 'Local Settings/': Permission denied
warning: could not open directory 'My Documents/': Permission denied
warning: could not open directory 'NetHood/': Permission denied
warning: could not open directory 'PrintHood/': Permission denied
warning: could not open directory 'Recent/': Permission denied
warning: could not open directory 'SendTo/': Permission denied
warning: could not open directory 'Start Menu/': Permission denied
warning: could not open directory 'Templates/': Permission denied
On branch master
No commits yet
Changes to be committed:
(use "git rm --cached <file>..." to unstage)
new file: .ipynb_checkpoints/Untitled3-checkpoint.ipynb
new file: .ipython/profile_default/history.sqlite
new file: .vscode/extensions/ritwickdey.liveserver-5.7.9/package.json
Untracked files:
(use "git add <file>..." to include in what will be committed)
...
.gitconfig
AppData/
Contacts/
Desktop/
Documents/
Downloads/
Favorites/
Jedi/
Links/
Music/
NTUSER.DAT
NTUSER.DAT{716b6697-d480-11ec-94d6-a6cb731d3b8d}.TxR.0.regtrans-ms
NTUSER.DAT{716b6697-d480-11ec-94d6-a6cb731d3b8d}.TxR.1.regtrans-ms
NTUSER.DAT{716b6697-d480-11ec-94d6-a6cb731d3b8d}.TxR.2.regtrans-ms
NTUSER.DAT{716b6697-d480-11ec-94d6-a6cb731d3b8d}.TxR.blf
NTUSER.DAT{716b6698-d480-11ec-94d6-a6cb731d3b8d}.TM.blf
NTUSER.DAT{716b6698-d480-11ec-94d6-a6cb731d3b8d}.TMContainer00000000000000000001.regtrans-ms
NTUSER.DAT{716b6698-d480-11ec-94d6-a6cb731d3b8d}.TMContainer00000000000000000002.regtrans-ms
OneDrive/
Pictures/
PycharmProjects/
Saved Games/
Searches/
Videos/
anaconda3/
coursera-test/
ntuser.dat.LOG1
ntuser.dat.LOG2
ntuser.ini
C:\Users\user>git rm --cached<file>Jedi/
The system cannot find the file specified.
C:\Users\user>git rm--cached<file>Music/...
The system cannot find the file specified.
C:\Users\user>git rm--cached<file>.ipynb_checkpoints/Untitled3-checkpoint.ipynb
The system cannot find the file specified.
I expected to load the HTML file to git hub and create my first web page, instead uploaded what seems to be my directory from c: drive and now I cannot unstage