One of the main problems here is that if you setup a webapp that issues OS commands, it will run under the security context of the webapp server. Depending on the webapp server and the level of paranoia of the server administrators, this could actually give you less abilities than a real shell user would have or it could give you more - including the ability to seriously dames the OS, expose it and other servers on the network to attackers and sof forth.
A better way to learn Unix commands is to get someone to set up a remote shell account. These days "ssh" is very popular. You can get ssh client software for Windows, including a free program called puTTY.
An IDE is no substitute for an Intelligent Developer.