Many many many changes, renamed directories, etc.
Merge branch 'master' of https://github.com/evolvedmicrobe/FreqSeq

Conflicts:
	TestData/LonAnalysis - Copy.xml
	TestData/freq2.xml
	afseqc/bin/Debug/freq2.xml
	afseqc/bin/Release/LonAnalysis - Copy.xml
	afseqc/freqseqc.csproj
	freqout/Properties/AssemblyInfo.cs
	freqout/afseqc.csproj.DotSettings.user
	freqout/bin/Debug/AF_Seq_Results.csv
	freqout/bin/Debug/FreqSeq.dll.mdb
	freqout/bin/Debug/afseqc.vshost.exe.manifest
	freqout/bin/Debug/freq.xml
	freqout/bin/Debug/freqseqc.exe.mdb
	freqout/bin/Release/LonAnalysis - Copy.xml
	freqout/bin/Release/LonAnalysis.xml
	freqout/bin/Release/Sample_1_run1_R1.fastq
	freqout/bin/Release/freq2.xml
	freqout/bin/Release/freqseqc.vshost.exe.manifest
	freqout/freqout.csproj
	freqout/freqout.csproj.user
	freqout/freqseqc.csproj
	freqout/obj/x86/Debug/.NETFramework,Version=v4.0,Profile=Client.AssemblyAttribute.cs
	freqout/obj/x86/Debug/afseqc.csproj.FileListAbsolute.txt
	freqout/obj/x86/Debug/freqseqc.csproj.FilesWrittenAbsolute.txt
	freqout/obj/x86/Debug/freqseqc.exe.mdb
	freqout/obj/x86/Release/afseqc.csproj.FileListAbsolute.txt
	freqout/obj/x86/Release/freqseqc.csproj.FileListAbsolute.txt