diff --git a/.gitignore b/.gitignore
index 7a67ce5..fdd1ee7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,5 @@
 build/a.lst
 build/a.rim
 build/image.fs
+build/bin
+build/n.out
diff --git a/Makefile b/Makefile
index 0913396..96837ec 100644
--- a/Makefile
+++ b/Makefile
@@ -1,31 +1,11 @@
-# Top level makefile to build the tests and everything else
-AS=tools/as7
-ASARGS=--format=ptr
-TESTDIR=tests
 
-all: buildit testit
+all: buildit
 
 buildit:
-	cd build && make
+	cd build && make all
 
-runsh: all
-	cd bin && ../tools/a7out sh
-
-testit:
-	mkdir -p $(TESTDIR)
-	$(AS) $(ASARGS) -o $(TESTDIR)/decimal_out  src/tests/decimal_out.s	
-	$(AS) $(ASARGS) -o $(TESTDIR)/fork_test    src/tests/fork_test.s	
-	$(AS) $(ASARGS) -o $(TESTDIR)/octal_test   src/tests/octal_test.s	
-	$(AS) $(ASARGS) -o $(TESTDIR)/testmul      src/tests/testmul.s
-	$(AS) $(ASARGS) -o $(TESTDIR)/write_test   src/tests/write_test.s
-
-runtests: tests
-	cd tests && ../tools/a7out decimal_out
-	cd tests && ../tools/a7out fork_test
-	cd tests && ../tools/a7out octal_test
-#	cd tests && ../tools/a7out testmul
-#	cd tests && ../tools/a7out write_test
+run:
+	cd build && make run
 
 clean:
-	rm -rf $(TESTDIR)/*
 	cd build && make clean
diff --git a/README.md b/README.md
index ec81851..276464f 100644
--- a/README.md
+++ b/README.md
@@ -25,19 +25,92 @@ system fully up on a PDP-7 system, fix any bugs and document everything.
 We have a [real PDP-7](http://physics.uoregon.edu/outreach/movies/pdplives/)
 and [SimH](http://simh.trailing-edge.com/) as target platforms.
 
+## Running pdp7-unix
+
+You will need [simh](http://simh.trailing-edge.com/) 4.0 to run pdp7-unix.  You can get the source code [here](https://github.com/simh/simh).  To compile it:
+
+`make pdp7`
+
+to run pdp-unix from the pdp7-unix source tree
+
+`make run`
+
+Press `ctl-e` to break out the simulator into simh
+
+A typical pdp7-unix on simh looks like:
+
+<pre>
+pdp7 unixv0.simh
+
+PDP-7 simulator V4.0-0 Beta        git commit id: e153b7f2
+CPU	idle disabled
+	8192W, EAE
+RB: buffering file in memory
+PDP-7 simulator configuration
+
+CPU	idle disabled
+CLK	60Hz, devno=00
+PTR	devno=01
+PTP	devno=02
+TTI	devno=03
+TTO	devno=04
+LPT	devno=65-66
+DRM	disabled
+RB	devno=71
+DT	devno=75-76, 8 units
+
+login: ken
+password: ken
+@ ln dd ken .
+@ ls
+dd      
+system  
+hello   
+.       
+@ ls system
+dd      
+ttyin   
+keyboard
+pptin   
+ttyout  
+display 
+pptout  
+as      
+cat     
+chmod   
+chown   
+chrm    
+cp      
+date    
+ds      
+ed      
+init    
+ln      
+ls      
+mv      
+password
+sh      
+stat    
+@ cat hello
+Hello, world
+@ 
+</pre>
+
+
 ## Source Tree
 
 The code in the original scans are (c) Novell who own the rights to the Unix
 source code. Everything that didn't come from the scanned files is GPLv3.
 
+* /build     is an area to build the kernel & filesystem and run them
+* /man		 holds man pages
+* /misc	     holds miscellaneous notes and information
 * /scans     holds the unmodified OCR versions of the scanned files
 * /src/cmd   holds the modified source code of the user-mode programs
 * /src/sys   holds the modified source code of the kernel
 * /src/other holds PDP-7 source code which did not come from the scanned files
 * /tools     holds the source for the tools written to assist the project
-* /build     is an area to build the kernel & filesystem and run them
-* /misc	     holds miscellaneous notes and information
-* /pdp7parse holds a Java parser for pdp7 source code
+
 
 ## Travis Status
 
diff --git a/build/Makefile b/build/Makefile
index 0d31b31..2d2f8e8 100644
--- a/build/Makefile
+++ b/build/Makefile
@@ -1,19 +1,29 @@
 # Build the kernel, the utilities, the filesystem and run SimH
 
+# tools
 AS=../tools/as7
 ASARGS=--format=ptr
 MKFS=../tools/mkfs7
+A7OUT=../tools/a7out 
+FSCK=../tools/fsck7
+PDP7=pdp7
 
+# source dirs
 SYSSRC=../src/sys
 CMDSRC=../src/cmd
 OTHERSRC=../src/other
-BINDIR=../bin
+TESTSRC=../src/tests
 
-all: cmd others a.rim image.fs
+# targets
+BINDIR=bin
+TESTDIR=tests
+IMAGEFILE=image.fs
+
+all: cmd others a.rim image
 
 # Manually make all before make run
-run:
-	pdp7 unixv0.simh
+run: clean all
+	$(PDP7) unixv0.simh
 
 a.rim:
 	$(AS) -f rim  -o a.rim $(SYSSRC)/sop.s $(SYSSRC)/s[1-8].s
@@ -23,11 +33,14 @@ coldboot:
 	$(AS) -f rim  -o a.rim $(SYSSRC)/sop.s $(SYSSRC)/s[1-9].s
 	$(AS) -n -f list -o a.lst $(SYSSRC)/sop.s $(SYSSRC)/s[1-9].s
 
-image.fs:
+image:
 	$(MKFS) --format simh proto
+	$(FSCK) $(IMAGEFILE)
 
 clean:
-	rm -f a.rim image.fs a.lst n.out $(BINDIR)/*
+	rm -f a.rim $(IMAGEFILE) a.lst n.out
+	rm -rf $(BINDIR)
+	rm -rf $(TESTDIR)
 
 dirs:
 	mkdir -p $(BINDIR)
@@ -55,6 +68,8 @@ cmd: dirs
 #	$(AS) $(ASARGS) -o $(BINDIR)/dsw    $(CMDSRC)/dsw.s
 	$(AS) $(ASARGS) -o $(BINDIR)/ed     $(CMDSRC)/ed1.s $(CMDSRC)/ed2.s
 	$(AS) $(ASARGS) -o $(BINDIR)/init   $(CMDSRC)/init.s
+	$(AS) $(ASARGS) -o $(BINDIR)/maksys $(CMDSRC)/maksys.s
+	$(AS) $(ASARGS) -o $(BINDIR)/trysys $(CMDSRC)/trysys.s
 
 others: dirs
 	$(AS) $(ASARGS) -o $(BINDIR)/sh    	$(OTHERSRC)/pbsh.s	
@@ -63,6 +78,22 @@ others: dirs
 	$(AS) $(ASARGS) -o $(BINDIR)/wktcp	$(OTHERSRC)/wktcp.s	
 	$(AS) $(ASARGS) -o $(BINDIR)/date  	$(OTHERSRC)/wktdate.s	
 	$(AS) $(ASARGS) -o $(BINDIR)/ln  	$(OTHERSRC)/wktln.s
-	$(AS) $(ASARGS) -o $(BINDIR)/ls  	$(OTHERSRC)/wktls.s		
 	$(AS) $(ASARGS) -o $(BINDIR)/mv    	$(OTHERSRC)/wktmv.s	
 	$(AS) $(ASARGS) -o $(BINDIR)/stat  	$(OTHERSRC)/wktstat.s	
+
+tests:
+	mkdir -p $(TESTDIR)
+	$(AS) $(ASARGS) -o $(TESTDIR)/decimal_out  $(TESTSRC)/decimal_out.s	
+	$(AS) $(ASARGS) -o $(TESTDIR)/fork_test    $(TESTSRC)/fork_test.s	
+	$(AS) $(ASARGS) -o $(TESTDIR)/octal_test   $(TESTSRC)/octal_test.s	
+	$(AS) $(ASARGS) -o $(TESTDIR)/testmul      $(TESTSRC)/testmul.s
+	$(AS) $(ASARGS) -o $(TESTDIR)/write_test   $(TESTSRC)/write_test.s
+
+runtests: tests
+	$(A7OUT) $(TESTDIR)/decimal_out
+	$(A7OUT) $(TESTDIR)/fork_test
+	$(A7OUT) $(TESTDIR)/octal_test
+#	$(A7OUT) $(TESTDIR)/testmul
+#	$(A7OUT) $(TESTDIR)/write_test
+
+
diff --git a/build/hello b/build/fs/hello
similarity index 100%
rename from build/hello
rename to build/fs/hello
diff --git a/build/password b/build/fs/password
similarity index 100%
rename from build/password
rename to build/fs/password
diff --git a/build/proto b/build/proto
index a4f4bef..2d90dbc 100644
--- a/build/proto
+++ b/build/proto
@@ -19,26 +19,26 @@ dd 	         drwr- -1 4
         ttyout   irwr- -1 11
         display  irwr- -1 12
         pptout   irwr- -1 13
-        as       frwr- -1 ../bin/as
-        cat      frwr- -1 ../bin/cat
-        chmod    frwr- -1 ../bin/chmod
-        chown    frwr- -1 ../bin/chown
-        chrm     frwr- -1 ../bin/chrm
-        cp       frwr- -1 ../bin/cp
-        date     frwr- -1 ../bin/date
-        ds       frwr- -1 ../bin/ds
-        ed       frwr- -1 ../bin/ed
-	init     frwr- -1 ../bin/init
-        ln       frwr- -1 ../bin/ln
-        ls       frwr- -1 ../bin/ls
-        mv       frwr- -1 ../bin/mv
-	password frw-- -1 password
-        sh       frwr- -1 ../bin/sh
-        stat     frwr- -1 ../bin/stat
+        as       frwr- -1 bin/as
+        cat      frwr- -1 bin/cat
+        chmod    frwr- -1 bin/chmod
+        chown    frwr- -1 bin/chown
+        chrm     frwr- -1 bin/chrm
+        cp       frwr- -1 bin/cp
+        date     frwr- -1 bin/date
+        ds       frwr- -1 bin/ds
+        ed       frwr- -1 bin/ed
+	init     frwr- -1 bin/init
+        ln       frwr- -1 bin/ln
+        ls       frwr- -1 bin/ls
+        mv       frwr- -1 bin/mv
+	password frw-- -1 fs/password
+        sh       frwr- -1 bin/sh
+        stat     frwr- -1 bin/stat
 	$
     ken      drwr- 10
       system l----  3
-        hello     frwr- 10 hello
+        hello     frwr- 10 fs/hello
       $
     dmr      drwr- 12
       system l----  3