Integrity checks and recovery

If I were to pin a file/directory e.g. `ipfs pin add /ipfs/QmYwAPJzv5CZsnA625s3Xf2nemtYgPpHdWEz79ojWnPbdG` and the `~/.ipfs` directory were to get **corrupted or edited** for whatever reason. Trying to access these files would lead to the error
`Error: incorrectly formatted merkledag node: Unmarshal failed. unexpected EOF`

I cant even run an `ipfs pin rm /ipfs/QmYwAPJzv5CZsnA625s3Xf2nemtYgPpHdWEz79ojWnPbdG`
The easiest way to fix this is to delete the `.ipfs` directory and run `ipfs init`.
It would be great if there was a repair command or something automatic.

Start by reproducing the corruption scenario with `ipfs pin add`, access to the pinned path, and `ipfs pin rm`, then compare the failure with recreating the repository via `ipfs init`. The issue is complete when corrupted or edited `~/.ipfs` data can be diagnosed and recovered through a defined repair command or automatic recovery path without deleting the directory.

Written by the indexing model from the issue text.