Version 1.4 release preparation

[AlexTate]

• Update DGE scatter plots to add support for plotting features that have a count of 0 in one condition. Currently these features are omitted from the plot due to the log2 singularity at 0
• Remove counter_all_features from the Run Config. This is a deprecated feature.
• Remove bowtie's trim5 and trim3 parameters from the Run Config to avoid confusion with tiny-collapse's 5p_trim and 3p_trim
• Update documentation diagrams to include the Mismatches column from the Features Sheet