Linux doesn't keep a "modified" flag for files - it keeps a timestamp. The DOS "modified" bit was handy for a single-user-system - the backup programs could set/reset it. But the Unix people tend to do things that are more devious.
There are a couple of options.
1. Check the original date against the change (modified) date. However, unlike the DOS Modified flag, there's no way to switch this off after you've done whatever operation is interested in modified files. Once modified, it's "modified" forever.
2. Check the change date against an absolute date. A number of *n*x utilities, including find and tar can do that, as well as bash builtin functions. This is what's usually used for incremental or differential backups.
There's also some tricks that involve keeping inventory of dates, but they're more specialized.
An IDE is no substitute for an Intelligent Developer.