Improved BBD9000init bootstrap. Removed hard-coded run files

Run directory specified in config used by all sub-processes to get
to fifos, etc. The shmem path is specified with env variable BBD9000_SHMEM.
BBD9000init will report BBD9000_SHMEM if run with shmem already existing.
Using sizeof instead defines for string lengths.
ilenced compiler warnings: signedness, unused vars, etc.
Cleaned up Makefile
Flowmeter calibration with more precision
Changed all SmartIO hex files to be for ATmega324pa
Clarified the bootstrapping comments
Fixed reversed TTL Rx/Tx
Fixed olinuxino header pin#s & GND
right angle headers twere oo close to each other

Moved the keypad and lcd headers another ~0.150 mil appart
More copper to traces, zones
Upped firmware vers. string to 3.3.3
Added errata for 3.3.2->3.3.3
Fixed adc calibration function
changed calibration settings
Changed R18 to 5k to make Vref 3.3V
Change drilli sze in C21 and R10 components
Fixed assy. spreadsheet and BOM to reflect 2.5V->3.3V Vref
Simplified traces, added copper where possible
Added UPS charge current limiter, U7 on +5Vout

Simple current limiter using two 75 ohm 3W resistors in parallel with a
diode - charging through 37.5 ohm/6W, discharge through diode.