A directive used to tell someone to straighten out their life. The sentence can also be modified to state that the speaker has solved their problems and/or chaos no longer dominates their life, i.e.: "I got my shit in line." The statement is an evolution of the phrase "ducks in a row."
I heard you got so wasted at Anthony's party that you came to on your ex's lawn 7 miles away two days later. Fuck! You'd better get your shit in line before you catch another case.