freechargecontroller.org schematic diagram. Power Assembly
The purpose of M1 is to stop the battery from discharging into the solar panel when its voltage drops in low light. M1's Source and Drain are connected 'backwards' so that its body diode will be turned off (whereas M2's body diode will be turned on under those conditions). Resistor R1 discharges M1's Gate capacitance to ensure that the FET turns off when there is no PWM drive, while D1 keeps it charged up during normal operation. In effect M1 is acting as a blocking diode, but with lower loss.

The VS line is 'ground' for the high-side driver's output circuit. M2's Gate drive voltage toggles between VS and the 'bootstrap' voltage at VB (produced by D2 and C2).

C11 and C3 filter out noise on the power supply to IC2. They may appear to be duplicating the function of C10 and C4, but do the job better by being physically closer to IC2.