add missing hidden files

.hgignore

+^mx.fastr/env
+^mx.fastr/checkstyle-timestamps
+^mx.fastr/eclipseinit.timestamp
+^mx.fastr/netbeansinit.timestamp
+^mx.fastr/eclipse-launches
+^mx.fastr/currentAnnotationProcessors
+^mx.fastr/ecj.jar
+^mx.fastr/eclipse-config-libs.zip
+^mx.fastr/eclipse-config.zip
+^mx.fastr/netbeans-config.zip
+^build/
+^build-nograal/
+^dist/
+^java/
+^lib/
+^jdk1.(7|8).0
+^java64/
+^work/
+\.checkstyle$
+\.classpath
+\.factorypath
+\.externalToolBuilders
+\.project
+\.settings/
+\.metadata/
+~$
+.gdb_history
+\.swo$
+\.csv$
+\.iml$
+\.swp$
+\.class$
+\.log$
+\.bak$
+\.aux$
+\.pdf$
+\.dot$
+\.pyc$
+\.hprof$
+\javafilelist.txt$
+\.hprof\.txt$
+^graal/.*/build.xml
+^.*/build.xml
+^.*/nbproject/
+dist
+^doc/.*/dot_temp_
+^doc/doxygen/.*$
+\.orig$
+output\.txt$
+output\.cfg$
+\.cfg
+/nbproject/private/
+^scratch/
+^test-output/
+scratch/
+bin/
+src_gen/
+^local/
+^.hgtip
+.DS_Store
+javadoc/
+.idea/
+^cscope.out
+^tags
+syntax: glob
+*.bgv
+core.*
+*.jar
+*.jar.*
+eclipse-build.xml
+rebuild-launch.out
+coverage
+jacoco.exec
+workingsets.xml
+.buildbot/
+graal.options
+agent/build/*
+agent/make/filelist
+agent/make/sa17.tar.gz
+.RData
+.Rhistory
+R.tokens
+.tmp.unit.knucleotide.input

mx.fastr/.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>mx.fastr</name>
+	<comment></comment>
+	<projects>
+		<project>mxtool</project>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>