improvements to clams CLI and app-dev template documentation

[keighrim]

closes#146

[codecov]

Codecov Report

Merging #148 (dc3e684) into develop (47ff9c8) will decrease coverage by 0.86%.
The diff coverage is 51.11%.

@@ Coverage Diff @@## develop #148 +/- ##
===========================================
- Coverage 77.89% 77.03% -0.86% 
===========================================
Files 7 7 Lines 579 601 +22 ===========================================
+ Hits 451 463 +12 - Misses 128 138 +10 

Flag	Coverage Δ
unittests	77.03% <51.11%> (-0.86%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
clams/develop/__init__.py	38.35% <37.14%> (+3.17%)	⬆️
clams/__init__.py	70.96% <100.00%> (-1.76%)	⬇️
clams/source/__init__.py	70.58% <100.00%> (+1.51%)	⬆️