Flatten documentation structure to a single directory

docs/Makefile

@@ -4,9 +4,9 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = PSOT-proteinsequenceobservationtool
-SOURCEDIR     = source
-BUILDDIR      = build
+SPHINXPROJ    = psot
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/make.bat

@@ -7,9 +7,9 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=python -msphinx
 )
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=PSOT-proteinsequenceobservationtool
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=psot
 
 if "%1" == "" goto help