Fix functions and Vignettes. update to 0.6.0

[chyang23]

What

This PR fixed errors in functions that make the data simulation run successfully in each scenario. The Vignettes are updated with no error in the devtool check results.

How

• Implemented if statements to ensure all conditions are met in the simulation process.
• Remove the metadata section when generating the sim_sce to avoid the replicated steps.
• Added an if statement to calculate the counts for sequencing to fix the error when the "totalDepth" exceeds the maximum allowance when simulating large cell samples.
  -Modified the ways to do large cell size simulation.

Sidenotes

Also updated the appropriate parameter descriptions and Removed unused packages in the Description file.