load custom GTR via CLI and bug fixes

• fix bug that omitted the inferred state of the root in the nexus export of the migration command
• add CLI flag and functionality to load sequence evolution models inferred and saved by TreeTime as human-readable text files. The flag is --custom-gtr <filename> and overwrites any arguments passed under the --gtr flag.
• explicitly specify the optimization method, brackets, bounds, and tolerances in calls of scipy.optimize.minimize to suppress scipy warning. Scipy had previously silently ignored bounds when the method wasn't explicitly set to bounded.