If correctly installed, the .git directory would be there. Maybe you've copied "everything" within the NodeBB directory at one time and since directories starting with . are hidden by default, you've lost this during it.
And if the .git directory is there, the update commands within the docs make sense. npm update (more specific npm install --production, which does include package update) gets called during the ./nodebb upgrade command.
I had back this problem a 2nd time 2 days ago, I don't know if it's related but I was doing iptables FW settings on the VM, I had nodeBB running, and also redis and from my computer desktop redis desktop manager connected to DB.
Then I made a mistake in iptables, blocked all redis port (even local), saying nodebb unable to connect to redis (so as redis desktop manager) then when I openned back 6379 port, all data was gone, not sure if it's related, just an information.
@julian but the point is that I haven't modified any of those files. Most of the files were text files like for example: README.md, LICENSE, etc.
Why would I modify any of those?
Tweaked settings in admin control panel
Tried to update to 0.7.3 -> got errors
Actually I got help from Nodebbs IRC- channel on how to resolve these errors with git and I'm now running 0.7.3. but it was not easy, I've no experience with git and no idea why I have to deal with stuff like this when updating.
Please do this! We need more tutorials and technical guides. I've been trying to immerse myself more in the source and writing plugins so I can write some stuff for the community.
(without these two lines you will get errors when you try to display the main page because Apache adds "index.html" by default to the request which gets then handled by Nodebb because of the two lines below these first two - but there is no index.html to handle because of the way Nodebb is built)
NC = ignore case
P = proxy, so that it is invisible to the user (they don't see the :4567)
L = last rule, we stop if match is found
Third line matches only your host without the trailing /somepage.html or /images/someimage.png or what ever. And the last line replaces that with some.example.com:4567/ and adds the rest of the address with $1
This is rather useful if you are already running other websites besides the Nodebb forums with Apache on the same server. Because if you use the instructions in the documentation for ProxyPass you will get all of your web traffic rerouted with that configuration (unless you are running Nodebb from a subfolder, I think?)