Cleanup various issues in markdown files.

COPYRIGHT.md

@@ -20,28 +20,51 @@ This Software includes and/or makes use of the following Third-Party
 Software subject to its own license:
 
 1. ROSE Compiler Framework (http://rosecompiler.org/)
+
    Copyright 2017 LLNL
+
    http://rosecompiler.org/ROSE_HTML_Reference/group__license.html
+
 2. XSB (http://xsb.sourceforge.net/)
+
    Copyright (C) The Research Foundation of SUNY, 1986, 1993-2013
+
    Copyright (C) ECRC, Germany, 1990
+
    https://sourceforge.net/p/xsb/src/HEAD/tree/trunk/XSB/LICENSE
+
 3. Boost (http://www.boost.org/)
+
    Copyright by various individual authors (see specific modules)
+
    http://www.boost.org/users/license.html
+
 4. yaml-cpp (https://github.com/jbeder/yaml-cpp)
+
    Copyright (c) 2008-2015 Jesse Beder
+
    https://github.com/jbeder/yaml-cpp/blob/master/LICENSE
+
 5. SQLLite (https://www.sqlite.org/)
+
    Public Domain
+
    https://www.sqlite.org/copyright.html
+
 6. GoogleTest (https://github.com/google/googletest)
+
    Copyright 2008, Google Inc
+
    https://github.com/google/googletest/blob/master/googletest/LICENSE
+
 7. MD5 Implementation
+
    Copyright (c) 2001 Alexander Peslyak placed in the Public Domain
+
 8. Yices (optional) (http://yices.csl.sri.com/)
+
    Copyright 2016, SRI International
+
    http://yices.csl.sri.com/old/yices-newlicense.shtml
 
 DM17-0290

INSTALL.md

@@ -1,3 +1,5 @@
+# Building and Installing
+
 This file describes how to build and install the Pharos static
 analysis framework tools.
 
@@ -22,9 +24,7 @@ Building Pharos requires a C++11 compliant compiler.  If you attempt
 to build Pharos (successfully or not) we'd like to hear about you
 experiences, and may be able to help with various build issues.
 
----
 # Dependencies
----
 
 First several important dependencies must be built or installed,
 including:
@@ -51,7 +51,8 @@ and install all components.
 
 You can build Boost using these commands:
 
-```$ mkdir boost
+```
+$ mkdir boost
 $ cd boost
 $ wget https://dl.bintray.com/boostorg/release/1.64.0/source/boost_1_64_0.tar.bz2
 $ tar -xzvf boost_1_64_0.tar.bz2
@@ -71,7 +72,8 @@ update CMake or patch patch it by hand.
 You may be able to muddle through with the standard operating system
 packages under certain (unknown) circumstances.
 
-```$ sudo yum install boost boost-devel
+```
+$ sudo yum install boost boost-devel
 $ sudo apt install libboost-dev libboost-all-dev
 ```
 
@@ -81,7 +83,8 @@ YAML-cpp is also a C++ library, and has the same C++11 ABI compability
 concerns.  We're usually building off a fairly current git checkout of
 the yaml-cpp repository.  We build yaml-cpp using commands like these:
 
-```$ git clone https://github.com/jbeder/yaml-cpp.git yaml
+```
+$ git clone https://github.com/jbeder/yaml-cpp.git yaml
 $ mkdir yaml/build
 $ cd yaml/build
 $ cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..
@@ -91,7 +94,8 @@ $ make -j4 install
 
 Or you can try installing the standard opeating system distribution:
 
-```$ sudo yum install yaml-cpp yaml-cpp-devel
+```
+$ sudo yum install yaml-cpp yaml-cpp-devel
 $ sudo apt install libyaml-cpp0.5v5 libyaml-cpp-dev
 ```
 
@@ -107,7 +111,8 @@ After going to the Yices website (https://yices.csl.rsi.com/) and
 obtaining version ONE of the Linux 64-bit executable dsitribution, you
 can install YICES using the following commands:
 
-```$ cd /usr/local
+```
+$ cd /usr/local
 $ sudo tar -xzvf yices-1.0.40-x86_64-unknown-linux-gnu-static-gmp.tar.gz
 ```
 
@@ -130,15 +135,17 @@ rose-develop, so be sure to fetch the "development" version of ROSE.
 
 You can obtain the latest version of ROSE from:
 
-```$ git clone https://github.com/rose-compiler/rose-develop rose
+```
+$ git clone https://github.com/rose-compiler/rose-develop rose
 ```
 
 Which has a reasonable chance of working or only having minor issues.
 If you want to be conservative, and use the version of ROSE that was
 known to compile with the latest major commit to the Pharos
 repository, you can checkout this commit:
 
-```$ git checkout 8c8aebc30e9295f89ad4dfee8fe741c26e7e3353
+```
+$ git checkout 8c8aebc30e9295f89ad4dfee8fe741c26e7e3353
 ```
 
 You may also be able to distribution packages from the ROSE website,
@@ -151,24 +158,25 @@ flags option to specify C++11 is required for ABI compatibility with
 Pharos and other libraries.  We use a configure command very similar
 to this one:
 
-```$ ./build
+```
+$ ./build
 $ mkdir release
 $ cd release
-$ ../configure --prefix=/usr/local --with-java=no \
-  --with-yices=/usr/local/yices-1.0.40 --enable-languages=binaries \
-  --without-doxygen --enable-projects-directory \
+$ ../configure --prefix=/usr/local --with-java=no --without-doxygen \
+  --enable-languages=binaries --enable-projects-directory \
   --disable-tutorial-directory --disable-boost-version-check \
   --with-boost=/usr/local CXXFLAGS=-std=c++11 --with-yaml=/usr/local
 ```
 
 You will want to add --enable-static if you want to build Pharos tools
-statically later.  Boost and YAML are not really optional, although
-YICES might be (untested).  Disabling Java, doxygen, and the
-tutorials, but enabling binaries and projects is related to generating
-a minimal and therefore faster build, so those confuration options
-should be optional.  To build use:
+statically later.  Boost and YAML are not optional.  If you've chosen
+to build with YICES, add "--with-yices=/usr/local/yices-1.0.40".
+Disabling Java, doxygen, and the tutorials, but enabling binaries and
+projects is related to generating a minimal and therefore faster
+build, so those confuration options should be optional.  To build use:
 
-```$ make -j4
+```
+$ make -j4
 ```
 
 ROSE can consume a fair amount of RAM and CPU power during the build,
@@ -177,7 +185,8 @@ or old hardware.  Be patient and go have lunch. :-)
 
 To install ROSE, run:
 
-```$ sudo make -j4 install
+```
+$ sudo make -j4 install
 ```
 
 ## XSB
@@ -195,24 +204,27 @@ with the XSB develoeprs that need to be applied to the XSB
 distribution to function properly with the Pharos tools.  Apply those
 patches with the following command:
 
-```$ svn checkout https://sourceforge.net/p/xsb/src/HEAD/tree/ XSB
+```
+$ svn checkout https://sourceforge.net/p/xsb/src/HEAD/tree/ XSB
 $ svn checkout -r 9046
 $ patch -p1 /path/to/pharos/xsb.patch
 ```
 
 The build procedure for XSB is documented in their distribution, but
 the produce is roughly:
 
-```$ cd XSB/build
-$ ./configure
+```
+$ cd XSB/build
+$ ./configure --prefix=/usr/local
 $ ./makexsb
 $ sudo ./makexsb install
 ```
 
 There's an unexplained installation error in XSB that we've had to
 hack around with the following command:
 
-```$ sudo touch /usr/local/xsb-3.7.0/syslib/sysinitrc
+```
+$ sudo touch /usr/local/xsb-3.7.0/syslib/sysinitrc
 ```
 
 ## SQLLite
@@ -222,18 +234,18 @@ standard operating system distribution of SQLLite.  Because the
 SQLLite interface is not C++11 depdendent the ABI concerns do not
 apply to this package.
 
-```$ sudo yum install sqlite sqlite-devel
+```
+$ sudo yum install sqlite sqlite-devel
 $ sudo apt-get install libsqlite3-0 libsqlite3-dev 
 ```
----
 # Building Pharos
----
 
 If all of the dependencies have been built and properly installed,
 building Pharos should be pretty easy.  We use the standard CMake
 approach which boils down to:
 
-```$ mkdir build
+```
+$ mkdir build
 $ cd build
 $ cmake ..
 $ make -j4
@@ -247,16 +259,16 @@ If you want to run tests to ensure that your configuration has been
 properly and is producing results identical to ours, you can run
 tests with the following command:
 
-```$ ctest -j4
+```
+$ ctest -j4
 ```
 
----
 # Installing Pharos
----
 
 Installing should also be easy.  Simply type:
 
-```$ make intall
+```
+$ make intall
 ```
 
 The software installs into /usr/local by default, but can be

README.md

@@ -1,6 +1,4 @@
----
 # Pharos Static Analysis Framework
----
 
 The Pharos static analysis framework is a project of the Software
 Engineering Institute at Carnegie Mellon University.  The framework is
@@ -29,9 +27,7 @@ binary static analysis researchers, please feel free to contact Cory
 Cohen <cfc@cert.org> with questions you may have about this work.  I
 may be unable to respond in a timely manner, but I will do my best.
 
----
 # Pharos Static Analysis Tools
----
 
 ## APIAnalyzer