Deprecated htsjdk.samtools.apps package.

[lbergelson]

• deprecated TimeChannel and TimeRandomAccesFile
• these are two tools which were probably used for testing at some point but should not be part of the htsjdk distribution

Description

Please explain the changes you made here.
Explain the motivation for making this change. What existing problem does the pull request solve?

Checklist

• Code compiles correctly
• New tests covering changes and new functionality
• All tests passing
• Extended the README / documentation, if necessary
• Is not backward compatible (breaks binary or source compatibility)

[codecov-io]

Codecov Report

Merging #1250 into master will increase coverage by 0.003%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #1250       +/-   ##
===============================================
+ Coverage     69.384%   69.387%   +0.003%     
- Complexity      8157      8158        +1     
===============================================
  Files            548       548               
  Lines          32702     32702               
  Branches        5522      5522               
===============================================
+ Hits           22690     22691        +1     
  Misses          7794      7794               
+ Partials        2218      2217        -1

Impacted Files	Coverage Δ	Complexity Δ
...rc/main/java/htsjdk/samtools/apps/TimeChannel.java	0% <ø> (ø)	0 <0> (ø)	⬇️
...ava/htsjdk/samtools/apps/TimeRandomAccessFile.java	0% <ø> (ø)	0 <0> (ø)	⬇️
...va/htsjdk/samtools/sra/SRAIndexedSequenceFile.java	64.865% <0%> (+2.703%)	7% <0%> (+1%)	⬆️