Documentation updates and small changes to configuration.py

[AlexTate]

This PR contains the following changes to Configuration:

• tiny-config can now be executed as a standalone step, as intended. Previously it relied on entry.py invoked during top-level tiny commands
• Users can now change the order of their CSV configuration file columns and the internal shortnames for each column will be remapped accordingly

This PR contains the following documentation changes:

• The workflow diagram has been updated and the opening description has been slightly refined
• A section for tagged counting has been added to Counter.md
• Commandline help strings for tinyRNA utilities have been moved to Parameters.md. A brief description of each step and a link to detailed documentation (if it exists) has taken its place
• A section for tiny-deseq.r has been added to Parameters.md
• Added a small note about how to use a custom conda environment name during installation
• The pointing hands around the tutorial link are now unicode rather than GitHub-specific markdown
• The link to Counter.md for the Features Sheet section in Configuration.md is now slightly more helpful

Edit 6/26:

• Added a short section about parallelization and how to turn it off for early steps in Pipeline.md
• Added info about obtaining a processed Run Config to use with an alternative CWL runner in Pipeline.md

Edit 6/27:

• We have decided to start referring to Collapser, Counter, and Plotter by their commandline names to avoid confusion. This also extends to DESeq2 where we are referring to the step/wrapper rather than the DESeq2 R package. The workflow has been updated to reflect these changes as well. In Python files, I've decided to only change user-facing info (error messages and help strings) and some comments where it made sense. I've decided to not rename the files themselves or package structure for now
• Plots have been updated to include recent changes to font styles. A fresh selection and order has also been included in README.md

Closes #90

[taimontgomery]

Can you update the plots in the readme? Maybe replace shorter len_dist plot with a PCA plot and order them such that the len_dist plot comes first, followed by the PCA plot, then the bar plots, and lastly the scatter plot.

[AlexTate]

Can you update the plots in the readme? Maybe replace shorter len_dist plot with a PCA plot and order them such that the len_dist plot comes first, followed by the PCA plot, then the bar plots, and lastly the scatter plot.

Good idea. These changes, and those we discussed today, are now included with this PR