removing unnecessary .moa files, added to README.md, script to reconstruct moa steps from .moa/configs

[kiwiroy]

We only need from this pull request

./02_TagCounts/01_IndividualTagCounts/.moa
./02_TagCounts/01_IndividualTagCounts/.moa/local_bash_history
./02_TagCounts/01_IndividualTagCounts/.moa/config
./02_TagCounts/02_MergedTagCounts/.moa
./02_TagCounts/02_MergedTagCounts/.moa/config
./02_TagCounts/03_TagCountToFastq/.moa
./02_TagCounts/03_TagCountToFastq/.moa/config
./03_SAM/.moa
./03_SAM/.moa/config
./06_HapMap/.moa
./06_HapMap/.moa/config
./05_TBT/01_IndividualTBT/.moa
./05_TBT/01_IndividualTBT/.moa/config
./05_TBT/04_PivotMergedTaxaTBT/.moa
./05_TBT/04_PivotMergedTaxaTBT/.moa/config
./04_TOPM/.moa
./04_TOPM/.moa/config

I will merge this manually

[kiwiroy]

closes #1