Tendency flags should modify Jacobians

When turning off an implicit tendency, the corresponding Jacobians need to be set to zero. Currently the tendency flags (e.g. `zero_tendency`, `advection_test`, `prognostic_tke`) don't modify the Jacobians.

No files or tests are named. Start by locating the implementations of the zero_tendency, advection_test, and prognostic_tke flags and the Jacobian assembly; verify which implicit tendencies each flag disables. Done means the corresponding Jacobian entries are zero when those flags are turned off, with tests covering the affected flags.

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