So even though this has a completely reasonable answer already...
I had a similar problem where I'd made a backup of my .\SteamApps\common\ folder and reinstalled Steam, expecting that it would detect the ~1000 or so install directories - but because I'd deleted the app manifests in .\SteamApps\ it was showing that nothing was installed.
I could manually go through, click Install on each game, let it detect that the install files were already there - but that involved a lot of clicking, waiting and trying to figure out what games I'd previously installed.
So instead of doing that, I whipped up a Powershell script to do it for me. In a nutshell, it enumerates the folders in .\SteamApps\common\ and matches them up to app Names and IDs. It spits out a list for you to validate, and then creates an app manifest for each discovered game.