GP-5078: Improvements to Ghidra Module directory layout

GPL/DMG/README.md

@@ -0,0 +1 @@
+# DMG

GPL/DMG/certification.manifest

@@ -3,6 +3,7 @@
 ##MODULE IP: LGPL 2.1
 ##MODULE IP: Public Domain
 Module.manifest||Public Domain||||END|
+README.md||GHIDRA||||END|
 data/lib/csframework.jar||LGPL 2.1||||END|
 data/lib/hfsexplorer-0_21-src.zip||GPL 3||||END|
 data/lib/hfsx.jar||GPL 3||||END|

GPL/DemanglerGnu/README.md

@@ -0,0 +1 @@
+# DemanglerGnu

GPL/DemanglerGnu/certification.manifest

@@ -5,5 +5,5 @@
 ##MODULE IP: LGPL 3.0
 ##MODULE IP: Public Domain
 Module.manifest||Public Domain||||END|
+README.md||GHIDRA||||END|
 src/demangler_gnu_v2_24/README.txt||Public Domain||||END|
-src/demangler_gnu_v2_33_1/README.txt||Public Domain||||END|

GPL/GnuDisassembler/README.md

@@ -0,0 +1,27 @@
+# GnuDisassembler
+
+The GnuDisassembler extension module must be built using gradle prior to its use within Ghidra.
+
+This module provides the ability to leverage the binutils disassembler capabilities
+for various processors as a means of verifying Sleigh disassembler output syntax.
+
+To build this extension for Linux or macOS:
+
+1. If building for an installation of Ghidra, copy the appropriate source distribution of binutils 
+   into this module's root directory. If building within a git clone of the full Ghidra source, copy
+   binutils source distribution file into the `ghidra.bin/GPL/GnuDisassembler` directory.
+	   
+   The supported version and archive format is identified within the build.gradle file. If a 
+   different binutils distribution is used the build.gradle and/or buildGdis.gradle	may require 
+   modification.
+	   
+   The build requires the following packages to be installed:
+   * flex
+   * bison
+   * texinfo
+   * zlib1g-dev
+	   
+2. Run gradle from the module's root directory (see top of `build.gradle` file for specific 
+instructions). 
+
+This resulting gdis executable will be located in `build/os/<platform>`.

GPL/GnuDisassembler/README.txt

@@ -1,26 +0,0 @@
-The GnuDisassembler extension module must be built using gradle prior to its' use within Ghidra.
-
-This module provides the ability to leverage the binutils disassembler capabilities
-for various processors as a means of verifying Sleigh disassembler output syntax.
-
-To build this extension for Linux or Mac OS X:
-
-	1. If building for an installation of Ghidra, copy the appropriate source distribution of 
-	   binutils into this module's root directory.  If building within a git clone of the full
-	   Ghidra source, copy binutils source distribution file into the ghidra.bin/GPL/GnuDisassembler 
-	   directory.
-	   
-	   The supported version and archive format is identified within the build.gradle file.
-	   If a different binutils distribution is used the build.gradle and/or buildGdis.gradle
-	   may require modification.
-	   
-	   The build requires the following packages to be installed:
-	     * flex
-	     * bison
-	     * texinfo
-	     * zlib1g-dev
-	   
-	2. Run gradle from the module's root directory (see top of build.gradle file for
-	   specific instructions). 
-
-This resulting gdis executable will be located in build/os/<platform>.

GPL/GnuDisassembler/certification.manifest

@@ -3,7 +3,7 @@
 ##MODULE IP: Public Domain
 .gitignore||Public Domain||||END|
 Module.manifest||Public Domain||||END|
-README.txt||Public Domain||||END|
+README.md||GHIDRA||||END|
 data/arm_test1.s||Public Domain||||END|
 data/big.elf||Public Domain||||END|
 data/little.elf||Public Domain||||END|

Ghidra/Configurations/Public_Release/README.md

@@ -0,0 +1 @@
+# Public_Release

Ghidra/Configurations/Public_Release/certification.manifest

@@ -1,5 +1,6 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/PDB_SYMBOL_SERVER_URLS.pdburl||GHIDRA||||END|
 src/global/docs/ChangeHistory.html||GHIDRA||||END|
 src/global/docs/UserAgreement.html||GHIDRA||||END|

Ghidra/Debug/AnnotationValidator/README.md

@@ -0,0 +1 @@
+# AnnotationValidator

Ghidra/Debug/AnnotationValidator/certification.manifest

@@ -1,3 +1,4 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 src/main/resources/META-INF/services/javax.annotation.processing.Processor||GHIDRA||||END|

Ghidra/Debug/Debugger-agent-dbgeng/README.md

@@ -0,0 +1 @@
+# Debugger-agent-dbgeng

Ghidra/Debug/Debugger-agent-dbgeng/certification.manifest

@@ -2,6 +2,7 @@
 ##MODULE IP: Apache License 2.0
 ##MODULE IP: MIT
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/debugger-launchers/kernel-dbgeng.bat||GHIDRA||||END|
 data/debugger-launchers/local-dbgeng-attach.bat||GHIDRA||||END|
 data/debugger-launchers/local-dbgeng-ext.bat||GHIDRA||||END|

Ghidra/Debug/Debugger-agent-dbgmodel-traceloader/README.md

@@ -0,0 +1 @@
+# Debugger-agent-dbgmodel-traceloader

Ghidra/Debug/Debugger-agent-dbgmodel-traceloader/certification.manifest

@@ -1,3 +1,4 @@
 ##VERSION: 2.0
 ##MODULE IP: Apache License 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|

Ghidra/Debug/Debugger-agent-dbgmodel/README.md

@@ -0,0 +1 @@
+# Debugger-agent-dbgmodel

Ghidra/Debug/Debugger-agent-dbgmodel/certification.manifest

@@ -1,5 +1,6 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 src/javaprovider/def/javaprovider.def||GHIDRA||||END|
 src/javaprovider/rc/javaprovider.rc||GHIDRA||||END|
 src/main/resources/agent/dbgmodel/model/impl/dbgmodel_schema.xml||GHIDRA||||END|

Ghidra/Debug/Debugger-agent-frida/FridaNotes.txt

@@ -1,28 +0,0 @@
-Random Notes on the Implementation of Debugger-agent-frida
-
-- Building libfrida-core.so:
-	You can download libfrida-core.a for Frida by grabbing the latest frida-core-devkit for your OS from 
-		https://github.com/frida/frida/releases 
-    or by downloading the Frida source and running:
-		python3 devkit.py frida-core linux-x86_64 DEVKIT
-	from the "releng" directory. 
-	
-Ghidra needs a dynamically-loadable version of libfrida-core.a which you can generate by something like:
-
-	cp ghidra_wrapper.c into the directory with libfrida-core.a and frida-core.h (distro or DEVKIT)
-	g++ -shared ghidra_wrapper.c ./libfrida-core.a -o libfrida-core.so
-
-Libfrida-core.so should then be added to the jna.library.path or put someplace like /usr/lib/x86_64-linux-gnu, where it will get picked up by Native.load().
-
-- Frida Functionality
-	The most interesting bits of Frida are available as "methods" from the Objects Tree.  For instance, if you select a function and hit "M", you will get a dialog with available methods.  Selecting, for example, "intercept" will bring up a second dialog with the relevant parameters.  For many of these, you will want to provide your own Javascript "on" functions, e.g. onEnter for the Interceptor. Stalking is available on Threads and the individual thread entries. Scan, protect, and watch functions are available on Memory. You can also redirect the output to GhidraScript, although this relies on a bit of a hack.  If your Javascript "Name" parameter is something like "interpreter", prepend "interpreter<=" to the output from your Javascript, and the results will be passed to both the console and the script.
-	
-- State in Frida:
-	Commands in Frida are, generally speaking, not state-dependent, i.e. they do not depend on whether the target is running or not, only on whether the frida-agent thread is running. Many of the gum-based commands do, however, depend on ptrace.  If you have a ptrace-based debugger attached to the target, they will time out.  You can attach a debugger after Frida, but you will have to detach it to regain the gum-based functionality.  "Detach" in most debuggers includes "resume", so it is difficult to get state other than the "initial" state from the frida-agent injection point.  It would be nice if "disconnect" worked, but "disconnect" (i.e. detach without resuming) also leaves Frida in a partially disabled state.
-	
-- Errors in Frida
-	The cloaking logic in Frida, e.g. in gum_cloak_add_thread and gum_cloak_index_of_thread, is broken as of the writing of this note.  Gum_cloak_add_thread is called for every thread, and gum_cloak_index_of_thread returns a non-negative result for every call but the first.  As a result, every thread but one is cloaked, and enumerateThreads returns only a single thread. This is documented in Issue #625 for the frida-gum project.  A quick fix is to comment out the cloaking call in frida-gum/gum/gumprocess.c::gum_emit_thread_if_not_cloaked.  Obviously, this may have other undesirable effects, but...
-	
-	The logic in the ordering of exception handlers also appears to be broken (Issue #627). New handlers are appended to the queue, in most cases after gum_exceptor_handle_scope_exception and gum_quick_core_handle_crashed_js. Gum_exceptor_handle_scope_exception almost always returns TRUE, breaking out of the queue and causing any remaining handlers to be ignored. This means any handler added with Process.setExceptionHandler is likely to be ignored.  A quick fix is to modify gum_exceptor_add to use g_slist_prepend instead of g_slist_append.
-	
-	Not really an error, but worth noting: building libfrida-core.so from the source may result in a library with glib2.0 dependencies that are incompatible with the current version of Eclipse. The not-so-simple solution is to build Eclipse on the machine that you used to build libfrida-core.

Ghidra/Debug/Debugger-agent-frida/README.md

@@ -0,0 +1,58 @@
+# Debugger-agent-frida
+
+## Random Notes on the Implementation of Debugger-agent-frida
+
+Building libfrida-core.so:
+* You can download libfrida-core.a for Frida by grabbing the latest frida-core-devkit for your OS 
+  from https://github.com/frida/frida/releases or by downloading the Frida source and running:
+  `python3 devkit.py frida-core linux-x86_64 DEVKIT` from the `releng` directory. 
+	
+Ghidra needs a dynamically-loadable version of libfrida-core.a which you can generate by something like:
+```bash
+cp ghidra_wrapper.c into the directory with libfrida-core.a and frida-core.h (distro or DEVKIT)
+g++ -shared ghidra_wrapper.c ./libfrida-core.a -o libfrida-core.so
+```
+
+Libfrida-core.so should then be added to the `j`na.library.path`or put someplace like
+`/usr/lib/x86_64-linux-gnu`, where it will get picked up by `Native.load()`.
+
+### Frida Functionality
+The most interesting bits of Frida are available as "methods" from the Objects Tree.  For instance, 
+if you select a function and hit `M`, you will get a dialog with available methods.  Selecting, 
+for example, `intercept` will bring up a second dialog with the relevant parameters.  For many of 
+these, you will want to provide your own Javascript `on` functions, e.g. `onEnter` for the 
+Interceptor. Stalking is available on Threads and the individual thread entries. Scan, protect, and 
+watch functions are available on Memory. You can also redirect the output to GhidraScript, although
+this relies on a bit of a hack.  If your Javascript `Name` parameter is something like 
+`interpreter`, prepend `interpreter<=` to the output from your Javascript, and the results will be 
+passed to both the console and the script.
+	
+### State in Frida
+Commands in Frida are, generally speaking, not state-dependent, i.e. they do not depend on whether 
+the target is running or not, only on whether the frida-agent thread is running. Many of the 
+gum-based commands do, however, depend on ptrace.  If you have a ptrace-based debugger attached to 
+the target, they will time out.  You can attach a debugger after Frida, but you will have to detach 
+it to regain the gum-based functionality.  "Detach" in most debuggers includes "resume", so it is 
+difficult to get state other than the "initial" state from the frida-agent injection point.  It 
+would be nice if "disconnect" worked, but "disconnect" (i.e. detach without resuming) also leaves 
+Frida in a partially disabled state.
+	
+### Errors in Frida
+The cloaking logic in Frida, e.g. in `gum_cloak_add_thread` and `gum_cloak_index_of_thread`, is 
+broken as of the writing of this note.  `gum_cloak_add_thread` is called for every thread, and 
+`gum_cloak_index_of_thread` returns a non-negative result for every call but the first.  As a 
+result, every thread but one is cloaked, and `enumerateThreads`returns only a single thread. This is
+documented in `Issue #625` for the frida-gum project.  A quick fix is to comment out the cloaking 
+call in `frida-gum/gum/gumprocess.c::gum_emit_thread_if_not_cloaked`.  Obviously, this may have 
+other undesirable effects, but...
+	
+The logic in the ordering of exception handlers also appears to be broken (`Issue #627`). New 
+handlers are appended to the queue, in most cases after `gum_exceptor_handle_scope_exception` and 
+`gum_quick_core_handle_crashed_js`. `gum_exceptor_handle_scope_exception` almost always returns 
+`TRUE`, breaking out of the queue and causing any remaining handlers to be ignored. This means any 
+handler added with `Process.setExceptionHandler` is likely to be ignored.  A quick fix is to modify
+`gum_exceptor_add` to use `g_slist_prepend instead` of `g_slist_append`.
+	
+Not really an error, but worth noting: building `libfrida-core.so` from the source may result in a 
+library with glib2.0 dependencies that are incompatible with the current version of Eclipse. The 
+not-so-simple solution is to build Eclipse on the machine that you used to build `libfrida-core`.

Ghidra/Debug/Debugger-agent-frida/certification.manifest

@@ -1,8 +1,8 @@
 ##VERSION: 2.0
 ##MODULE IP: Apache License 2.0
 ##MODULE IP: Apache License 2.0 with LLVM Exceptions
-FridaNotes.txt||GHIDRA||||END|
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 build.gradle||GHIDRA||||END|
 data/scripts/onAccess.js||GHIDRA||||END|
 data/scripts/onAccessExt.js||GHIDRA||||END|

Ghidra/Debug/Debugger-agent-gdb/README.md

@@ -0,0 +1 @@
+# Debugger-agent-gdb

Ghidra/Debug/Debugger-agent-gdb/certification.manifest

@@ -1,6 +1,7 @@
 ##VERSION: 2.0
 ##MODULE IP: JSch License
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/debugger-launchers/local-gdb.bat||GHIDRA||||END|
 data/debugger-launchers/qemu-gdb.bat||GHIDRA||||END|
 data/debugger-launchers/raw-gdb.bat||GHIDRA||||END|

Ghidra/Debug/Debugger-agent-lldb/README.md

@@ -0,0 +1 @@
+# Debugger-agent-lldb

Ghidra/Debug/Debugger-agent-lldb/certification.manifest

@@ -2,6 +2,7 @@
 ##MODULE IP: Apache License 2.0
 ##MODULE IP: Apache License 2.0 with LLVM Exceptions
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 build.gradle||GHIDRA||||END|
 data/debugger-launchers/local-lldb.bat||GHIDRA||||END|
 src/llvm-project/lldb/bindings/java/java-typemaps.swig||Apache License 2.0 with LLVM Exceptions||||END|

Ghidra/Debug/Debugger-api/README.md

@@ -0,0 +1 @@
+# Debugger-api

Ghidra/Debug/Debugger-api/certification.manifest

@@ -1,2 +1,3 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|

Ghidra/Debug/Debugger-gadp/README.md

@@ -0,0 +1 @@
+# Debugger-gadp

Ghidra/Debug/Debugger-gadp/certification.manifest

@@ -1,2 +1,3 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|

Ghidra/Debug/Debugger-isf/README.md

@@ -0,0 +1 @@
+# Debugger-isf

Ghidra/Debug/Debugger-isf/build.gradle

@@ -31,11 +31,3 @@ dependencies {
 	testImplementation project(path: ':Framework-AsyncComm', configuration: 'testArtifacts')
 	testImplementation project(path: ':Framework-Debugging', configuration: 'testArtifacts')
 }
-
-// Include buildable native source in distribution
-rootProject.assembleDistribution {
-	from (this.project.projectDir.toString()) {
-		include "runISFServer"
-		into  { getZipPath(this.project) }
-	}
-}

Ghidra/Debug/Debugger-isf/certification.manifest

@@ -1,3 +1,4 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
-runISFServer||GHIDRA||||END|
+README.md||GHIDRA||||END|
+support/runISFServer||GHIDRA||||END|

Ghidra/Debug/Debugger-isf/support/runISFServer

@@ -26,9 +26,9 @@ VMARG_LIST="-XX:ParallelGCThreads=2 -XX:CICompilerCount=2 "
 # fallback, which doesn't attempt to do anything with links.
 SCRIPT_FILE="$(readlink -f "$0" 2>/dev/null || readlink "$0" 2>/dev/null || echo "$0")"
 SCRIPT_DIR="${SCRIPT_FILE%/*}"
-SUPPORT_DIR="${SCRIPT_DIR}/../../../support"
+SUPPORT_DIR="${SCRIPT_DIR}/../../../../support"
 if ! [ -f "${SUPPORT_DIR}/launch.properties" ]; then
-    SUPPORT_DIR="${SCRIPT_DIR}/../../RuntimeScripts/Linux/support"
+    SUPPORT_DIR="${SCRIPT_DIR}/../../../RuntimeScripts/Linux/support"
 fi
 
 # Launch ISF Server.

Ghidra/Debug/Debugger-jpda/README.md

@@ -0,0 +1 @@
+# Debugger-jpda

Ghidra/Debug/Debugger-jpda/certification.manifest

@@ -1,5 +1,6 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/debugger-launchers/attach-java.jsh||GHIDRA||||END|
 data/debugger-launchers/bypid-java.jsh||GHIDRA||||END|
 data/debugger-launchers/local-java.jsh||GHIDRA||||END|

Ghidra/Debug/Debugger-rmi-trace/README.md

@@ -0,0 +1 @@
+# Debugger-rmi-trace

Ghidra/Debug/Debugger-rmi-trace/certification.manifest

@@ -3,6 +3,7 @@
 ##MODULE IP: BSD-3-PSUTIL
 DEVNOTES.txt||GHIDRA||||END|
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||||END|
 src/main/help/help/topics/TraceRmiConnectionManagerPlugin/TraceRmiConnectionManagerPlugin.html||GHIDRA||||END|

Ghidra/Debug/Debugger-swig-lldb/README.md

@@ -0,0 +1 @@
+# Debugger-swig-lldb

Ghidra/Debug/Debugger-swig-lldb/certification.manifest

@@ -3,6 +3,7 @@
 ##MODULE IP: Apache License 2.0 with LLVM Exceptions
 InstructionsForBuildingLLDBInterface.txt||GHIDRA||||END|
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 build.gradle||GHIDRA||||END|
 src/llvm-project/lldb/bindings/java/java-typemaps.swig||Apache License 2.0 with LLVM Exceptions||||END|
 src/llvm-project/lldb/bindings/java/java.swig||Apache License 2.0 with LLVM Exceptions||||END|

Ghidra/Debug/Debugger/README.md

@@ -0,0 +1 @@
+# Debugger

Ghidra/Debug/Debugger/certification.manifest

@@ -5,6 +5,7 @@
 ##MODULE IP: Oxygen Icons - LGPL 3.0
 ##MODULE IP: Tango Icons - Public Domain
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 data/debugger.theme.properties||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||||END|

Ghidra/Debug/Framework-AsyncComm/README.md

@@ -0,0 +1 @@
+# Framework-AsyncComm

Ghidra/Debug/Framework-AsyncComm/certification.manifest

@@ -1,3 +1,4 @@
 ##VERSION: 2.0
 ##MODULE IP: BSD-3-GOOGLE
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|

Ghidra/Debug/Framework-Debugging/README.md

@@ -0,0 +1 @@
+# Framework-Debugging

Ghidra/Debug/Framework-Debugging/certification.manifest

@@ -1,6 +1,7 @@
 ##VERSION: 2.0
 ##MODULE IP: Apache License 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 src/main/resources/agent.log4j.xml||GHIDRA||||END|
 src/main/resources/log4j-appender-console.xml||GHIDRA||||END|

Ghidra/Debug/Framework-TraceModeling/README.md

@@ -0,0 +1 @@
+# Framework-TraceModeling

Ghidra/Debug/Framework-TraceModeling/certification.manifest

@@ -1,3 +1,4 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/tracemodeling.theme.properties||GHIDRA||||END|

Ghidra/Debug/ProposedUtils/README.md

@@ -0,0 +1 @@
+# ProposedUtils

Ghidra/Debug/ProposedUtils/certification.manifest

@@ -1,4 +1,5 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 build.gradle||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|

Ghidra/Extensions/BSimElasticPlugin/INSTALL.txt

@@ -1,99 +0,0 @@
-Installation of the Elasticsearch BSim Plug-in:
-
-In order to use Elasticsearch as the back-end database for a BSim instance,
-the lsh plug-in, included with this Ghidra extension, must be installed on
-the Elasticsearch cluster.
-
-The lsh plug-in is bundled in the standard plug-in format as the file
-'lsh.zip'.  It must be installed separately on EVERY node of the cluster,
-and each node must be restarted after the install in order for the plug-in to
-become active.
-
-For a single node, installation is accomplished with the command-line
-'elasticsearch-plugin' script that comes with the standard Elasticsearch
-distribution. It expects a URL pointing to the plug-in to be installed.
-The basic command, executed in the Elasticsearch installation directory
-for the node, is
-
-  bin/elasticsearch-plugin install file:///path/to/ghidra/Ghidra/Extensions/BSimElasticPlugin/data/lsh.zip
-
-Replace the initial portion of the absolute path in the URL to point to your
-particular Ghidra installation.
-
-Deployment:
-
-Follow the Elasticsearch documentation to do any additional configuration,
-starting, stopping, and management of your Elasticsearch cluster.
-
-To try BSim with a toy deployment, you can start a single node (as per the
-documentation) from the command-line by just running
-
-  bin/elasticsearch
-
-This will dump logging messages to the console, and you should see '[lsh]'
-listed among the loaded plug-ins as the node starts up.
-
-This will typically start the database with password authentication enabled.  An
-'elastic' user will be automatically created with a randomly generated password that
-gets printed to the console the first time the node is started.  To add additional
-users, use a curl command like
-
-curl -k -u elastic:XXXXXX -X POST "https://localhost:9200/_security/user/ghidrauser?pretty" -H 'Content-Type: application/json' -d'
-{
-  "password" : "changeme",
-  "roles" : [ "superuser" ],
-  "full_name" : "Ghidra User",
-  "email" : "ghidrauser@example.com"
-}
-'
-
-Replace XXXXXX with the generated password for the 'elastic' user.  This example
-creates a user 'ghidrauser', with administrator privileges. The built-in role
-'viewer' can be used to create users with read-only access to the database.
-
-Once the Elasticsearch node(s) are running, whether they are a toy or a full
-deployment, you can immediately proceed to the BSim 'bsim' command.
-The Ghidra/BSim client and 'bsim' command automatically assume an
-Elasticsearch server when they see the 'https' protocol in the provided URLs,
-although the 'elastic" protocol may also be specified and is equivalent.
-The use of the 'http' protocol for Elasticsearch is not supported.
-Adjust the hostname, port number, and repository name as appropriate. 
-Use a command-line similar to the following to create a BSim instance:
-
-  bsim createdatabase elastic://1.2.3.4:9200/repo medium_32
-  
-This is equivalent to:
-
-  bsim createdatabase https://1.2.3.4:9200/repo medium_32
-
-Use a command-line like this to generate and commit signatures from a Ghidra Server
-repository to the Elasticsearch database created above:
-
-  bsim generatesigs ghidra://1.2.3.4/repo --bsim elastic://1.2.3.4:9200/repo
-
-Within Ghidra's BSim client, enter the same URL into the database connection
-panel in order to place queries to your Elasticsearch deployment. See the BSim
-documentation included with Ghidra for full details.
-
-
-Version:
-
-The current BSim plug-in was tested with Elasticsearch version 8.8.1.
-A change to the Elasticsearch scripting interface, starting with version 7.15, makes the BSim
-plug-in incompatible with previous versions, but the lsh plug-in jars may work without change
-across later Elasticsearch versions.
-
-Elasticsearch plug-ins explicitly encode the version of Elasticsearch they work with, and the
-plug-in script will refuse to install the lsh plug-in if its version does not match your
-particular installation. If your Elasticsearch version is slightly different, you can try
-unpacking the zip file, changing the version number to match your software, and then repacking
-the zip file. Within the zip archive, the version number is stored in a configuration file
-
-  elasticsearch/plugin-descriptor.properties
-  
-The file format is fairly simple: edit the line
-
-  elasticsearch.version=8.8.1
-
-The plugin may work with other nearby versions, but proceed at your own risk.
-

Ghidra/Extensions/BSimElasticPlugin/README.md

@@ -0,0 +1,99 @@
+# BSimElasticPlugin
+
+## Installation of the Elasticsearch BSim Plug-in
+In order to use Elasticsearch as the back-end database for a BSim instance, the lsh plug-in, 
+included with this Ghidra extension, must be installed on the Elasticsearch cluster.
+
+The lsh plug-in is bundled in the standard plug-in format as the file `lsh.zip`. It must be 
+installed separately on EVERY node of the cluster, and each node must be restarted after the install
+in order for the plug-in to become active.
+
+For a single node, installation is accomplished with the command-line `elasticsearch-plugin` script
+that comes with the standard Elasticsearch distribution. It expects a URL pointing to the plug-in to
+be installed. The basic command, executed in the Elasticsearch installation directory for the node,
+is: 
+```
+bin/elasticsearch-plugin install file:///path/to/ghidra/Ghidra/Extensions/BSimElasticPlugin/data/lsh.zip
+```
+
+Replace the initial portion of the absolute path in the URL to point to your particular Ghidra 
+installation.
+
+## Deployment
+Follow the Elasticsearch documentation to do any additional configuration, starting, stopping, and 
+management of your Elasticsearch cluster.
+
+To try BSim with a toy deployment, you can start a single node (as per the documentation) from the 
+command-line by just running
+```
+bin/elasticsearch
+```
+
+This will dump logging messages to the console, and you should see `[lsh]` listed among the loaded 
+plug-ins as the node starts up.
+
+This will typically start the database with password authentication enabled.  An `elastic` user will
+be automatically created with a randomly generated password that gets printed to the console the 
+first time the node is started.  To add additional users, use a curl command like
+```
+curl -k -u elastic:XXXXXX -X POST "https://localhost:9200/_security/user/ghidrauser?pretty" -H 'Content-Type: application/json' -d'
+{
+  "password" : "changeme",
+  "roles" : [ "superuser" ],
+  "full_name" : "Ghidra User",
+  "email" : "ghidrauser@example.com"
+}
+```
+
+Replace `XXXXXX` with the generated password for the `elastic` user.  This example creates a user 
+`ghidrauser`, with administrator privileges. The built-in role `viewer` can be used to create users
+with read-only access to the database.
+
+Once the Elasticsearch node(s) are running, whether they are a toy or a full deployment, you can 
+immediately proceed to the BSim `bsim` command. The Ghidra/BSim client and `bsim` command 
+automatically assume an Elasticsearch server when they see the __https__ protocol in the provided 
+URLs, although the __elastic__ protocol may also be specified and is equivalent. The use of the 
+__http__ protocol for Elasticsearch is not supported. Adjust the hostname, port number, and 
+repository name as appropriate. Use a command-line similar to the following to create a BSim 
+instance:
+```
+bsim createdatabase elastic://1.2.3.4:9200/repo medium_32
+```
+
+This is equivalent to:
+```
+bsim createdatabase https://1.2.3.4:9200/repo medium_32
+```
+
+Use a command-line like this to generate and commit signatures from a Ghidra Server repository to 
+the Elasticsearch database created above:
+```
+bsim generatesigs ghidra://1.2.3.4/repo --bsim elastic://1.2.3.4:9200/repo
+```
+
+Within Ghidra's BSim client, enter the same URL into the database connection panel in order to place
+queries to your Elasticsearch deployment. See the BSim documentation included with Ghidra for full
+details.
+
+## Version
+
+The current BSim plug-in was tested with Elasticsearch version `8.8.1`. A change to the 
+Elasticsearch scripting interface, starting with version `7.15`, makes the BSim plug-in incompatible
+with previous versions, but the lsh plug-in jars may work without change across later Elasticsearch 
+versions.
+
+Elasticsearch plug-ins explicitly encode the version of Elasticsearch they work with, and the
+plug-in script will refuse to install the lsh plug-in if its version does not match your
+particular installation. If your Elasticsearch version is slightly different, you can try
+unpacking the zip file, changing the version number to match your software, and then repacking
+the zip file. Within the zip archive, the version number is stored in a configuration file
+```
+elasticsearch/plugin-descriptor.properties
+```
+
+The file format is fairly simple: edit the line
+```
+elasticsearch.version=8.8.1
+```
+
+The plugin may work with other nearby versions, but proceed at your own risk.

Ghidra/Extensions/BSimElasticPlugin/certification.manifest

@@ -1,6 +1,6 @@
 ##VERSION: 2.0
 ##MODULE IP: Apache License 2.0
-INSTALL.txt||GHIDRA||||END|
 Module.manifest||GHIDRA||reviewed||END|
+README.md||GHIDRA||||END|
 contribZipExclude/plugin-descriptor.properties||GHIDRA||||END|
 extension.properties||GHIDRA||||END|

Ghidra/Extensions/MachineLearning/README.md

@@ -0,0 +1 @@
+# MachineLearning

Ghidra/Extensions/MachineLearning/certification.manifest

@@ -3,8 +3,8 @@
 ##MODULE IP: BSD-2-ORACLE
 ##MODULE IP: BSD-3-GOOGLE
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 extension.properties||GHIDRA||||END|
-lib/README.txt||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||||END|
 src/main/help/help/topics/RandomForestFunctionFinderPlugin/RandomForestFunctionFinderPlugin.htm||GHIDRA||||END|
 src/main/resources/images/README.txt||GHIDRA||||END|

Ghidra/Extensions/SampleTablePlugin/README.md

@@ -0,0 +1 @@
+# SampleTablePlugin

Ghidra/Extensions/SampleTablePlugin/certification.manifest

@@ -2,6 +2,7 @@
 ##MODULE IP: FAMFAMFAM Icons - CC 2.5
 ##MODULE IP: Oxygen Icons - LGPL 3.0
 Module.manifest||GHIDRA||reviewed||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 data/sampletableplugin.theme.properties||GHIDRA||||END|
 extension.properties||GHIDRA||||END|

Ghidra/Extensions/SleighDevTools/README.md

@@ -0,0 +1 @@
+# SleighDevTools

Ghidra/Extensions/SleighDevTools/certification.manifest

@@ -1,5 +1,6 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 data/LanguageMap.txt||GHIDRA||||END|
 extension.properties||GHIDRA||||END|

Ghidra/Extensions/bundle_examples/README.md

@@ -0,0 +1 @@
+# bundle_examples

Ghidra/Extensions/bundle_examples/certification.manifest

@@ -1,5 +1,6 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 extension.properties||GHIDRA||||END|
 scripts_jar1/META-INF/MANIFEST.MF||GHIDRA||||END|
 scripts_jar2/META-INF/MANIFEST.MF||GHIDRA||||END|

Ghidra/Extensions/sample/README.md

@@ -0,0 +1 @@
+# sample

Ghidra/Extensions/sample/certification.manifest

@@ -2,6 +2,7 @@
 ##MODULE IP: FAMFAMFAM Icons - CC 2.5
 ##MODULE IP: Oxygen Icons - LGPL 3.0
 Module.manifest||GHIDRA||reviewed||END|
+README.md||GHIDRA||||END|
 data/README.txt||GHIDRA||||END|
 data/sample.theme.properties||GHIDRA||||END|
 extension.properties||GHIDRA||||END|

Ghidra/Features/BSim/README.md

@@ -0,0 +1 @@
+# BSim

Ghidra/Features/BSim/build.gradle

@@ -44,19 +44,18 @@ dependencies {
 // into common zip to allow for a rebuild of the postgres server if needed
 
 rootProject.assembleDistribution { 
+	def p = this.project
+	def zipPath = getZipPath(p)
 	
 	String postgresqlDepsFile = "${DEPS_DIR}/BSim/${postgresql_distro}"
 	String postgresqlBinRepoFile = "${BIN_REPO}/Ghidra/Features/BSim/${postgresql_distro}"
 		
 	def postgresqlFile = file(postgresqlDepsFile).exists() ? postgresqlDepsFile : postgresqlBinRepoFile
 	
-    into (getZipPath(this.project)) {
-		from file("make-postgres.sh")	
-	}
-	into (getZipPath(this.project)) {
+	into ("${zipPath}/support") {
 		from file(postgresqlFile)	
 	}
-	into (getZipPath(this.project)  + "/src/lshvector") {
+	into ("${zipPath}/src/lshvector") {
 		from files("src/lshvector")	
 	}
 }

Ghidra/Features/BSim/certification.manifest

@@ -11,6 +11,7 @@
 ##MODULE IP: PostgresqlJDBC License
 ##MODULE IP: Public Domain
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/bsim.theme.properties||GHIDRA||||END|
 data/large_32.xml||GHIDRA||||END|
 data/lshweights_32.xml||GHIDRA|||Signature data|END|

Ghidra/Features/BSim/src/main/help/help/topics/BSim/DatabaseConfiguration.html

@@ -104,7 +104,7 @@
               extension, provided as part of the Ghidra installation. Prebuilt servers, like those
               provided as OS distribution packages, will not work as is with BSim. For users on Linux
               and macOS, the Ghidra installation provides a script, <CODE>make-postgres.sh</CODE>,
-              in the module directory <CODE>Ghidra/Features/BSim</CODE> that builds both the PostgreSQL
+              in the module directory <CODE>Ghidra/Features/BSim/support</CODE> that builds both the PostgreSQL
               server and the BSim extension from source and prepares the installation for use with
               Ghidra.  If not already included in the Ghidra installation, the source distribution
               file, currently <CODE>postgresql-15.3.tar.gz</CODE>, can be obtained from the PostgreSQL
@@ -127,7 +127,7 @@
             <DIV class="informalexample">
               <TABLE border="0" summary="Simple list" class="simplelist">
                 <TR>
-                  <TD><CODE class="computeroutput">$(ROOT)/Ghidra/Features/BSim/postgresql-15.3.tar.gz
+                  <TD><CODE class="computeroutput">$(ROOT)/Ghidra/Features/BSim/support/postgresql-15.3.tar.gz
 		  </CODE></TD>
                 </TR>
               </TABLE>
@@ -138,7 +138,7 @@
             <DIV class="informalexample">
               <TABLE border="0" summary="Simple list" class="simplelist">
                 <TR>
-                  <TD><CODE class="computeroutput">cd $(ROOT)/Ghidra/Features/BSim
+                  <TD><CODE class="computeroutput">cd $(ROOT)/Ghidra/Features/BSim/support
 		  </CODE></TD>
                 </TR>
                 <TR>

Ghidra/Features/BSim/src/main/java/ghidra/features/bsim/query/BSimControlLaunchable.java

@@ -112,7 +112,8 @@ public class BSimControlLaunchable implements GhidraLaunchable {
 	}
 
 	private final static String POSTGRES = "postgresql";
-	private final static String POSTGRES_BUILD_SCRIPT = "Ghidra/Features/BSim/make-postgres.sh";
+	private final static String POSTGRES_BUILD_SCRIPT =
+		"Ghidra/Features/BSim/support/make-postgres.sh";
 	private final static String POSTGRES_CONFIGFILE = "postgresql.conf";
 	private final static String POSTGRES_CONNECTFILE = "pg_hba.conf";
 	private final static String POSTGRES_IDENTFILE = "pg_ident.conf";

Ghidra/Features/BSim/support/make-postgres.sh

@@ -50,11 +50,12 @@ POSTGRES=postgresql-15.3
 POSTGRES_GZ=${POSTGRES}.tar.gz
 POSTGRES_CONFIG_OPTIONS="--disable-rpath --with-openssl"
 
-DIR=$(cd `dirname $0`; pwd)
+DIR=$(cd `dirname $0`; pwd)/..
+echo $DIR
 
 POSTGRES_GZ_PATH=${DIR}/../../../../ghidra.bin/Ghidra/Features/BSim/${POSTGRES_GZ}
 if [ ! -f "${POSTGRES_GZ_PATH}" ]; then
-	POSTGRES_GZ_PATH=${DIR}/${POSTGRES_GZ}
+	POSTGRES_GZ_PATH=${DIR}/support/${POSTGRES_GZ}
 	if [ ! -f "${POSTGRES_GZ_PATH}" ]; then
 		echo "Postgres source bundle not found: ${POSTGRES_GZ_PATH}"
 		exit -1

Ghidra/Features/BSimFeatureVisualizer/README.md

@@ -0,0 +1 @@
+# BSimFeatureVisualizer

Ghidra/Features/BSimFeatureVisualizer/certification.manifest

@@ -1,5 +1,6 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/bsim.theme.properties||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||||END|
 src/main/help/help/topics/BSimFeatureVisualizerPlugin/BSimFeatureVisualizerPlugin.htm||GHIDRA||||END|

Ghidra/Features/Base/README.md

@@ -0,0 +1 @@
+# Base

Ghidra/Features/Base/certification.manifest

@@ -15,6 +15,7 @@
 .launch/Headless.launch||GHIDRA||||END|
 .launch/JShell.launch||GHIDRA||||END|
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ElfFunctionsThatDoNotReturn||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 data/GolangFunctionsThatDoNotReturn||GHIDRA||||END|

Ghidra/Features/BytePatterns/README.md

@@ -0,0 +1 @@
+# BytePatterns

Ghidra/Features/BytePatterns/certification.manifest

@@ -1,6 +1,7 @@
 ##VERSION: 2.0
 ##MODULE IP: Oxygen Icons - LGPL 3.0
 Module.manifest||GHIDRA||reviewed||END|
+README.md||GHIDRA||||END|
 data/bytepatterns.theme.properties||GHIDRA||||END|
 data/test/FileBitPatternInfoReaderTestFile1.xml||GHIDRA||||END|
 data/test/FileBitPatternInfoReaderTestFile2.xml||GHIDRA||||END|

Ghidra/Features/ByteViewer/README.md

@@ -0,0 +1 @@
+# ByteViewer

Ghidra/Features/ByteViewer/certification.manifest

@@ -2,6 +2,7 @@
 ##MODULE IP: FAMFAMFAM Icons - CC 2.5
 ##MODULE IP: Oxygen Icons - LGPL 3.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||reviewed||END|
 data/byteviewer.theme.properties||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||reviewed||END|

Ghidra/Features/CodeCompare/README.md

@@ -0,0 +1 @@
+# CodeCompare

Ghidra/Features/CodeCompare/certification.manifest

@@ -1,4 +1,5 @@
 ##VERSION: 2.0
 ##MODULE IP: LGPL 3.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/codecompare.theme.properties||GHIDRA||||END|

Ghidra/Features/DebugUtils/README.md

@@ -0,0 +1 @@
+# DebugUtils

Ghidra/Features/DebugUtils/certification.manifest

@@ -1,2 +1,3 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||reviewed||END|
+README.md||GHIDRA||||END|

Ghidra/Features/Decompiler/README.md

@@ -0,0 +1 @@
+# Decompiler

Ghidra/Features/Decompiler/certification.manifest

@@ -6,6 +6,7 @@
 ##MODULE IP: Tango Icons - Public Domain
 ##MODULE IP: zlib License
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/decompiler.theme.properties||GHIDRA||||END|
 src/decompile/.cproject||GHIDRA||||END|
 src/decompile/cpp/.gitignore||GHIDRA||||END|

Ghidra/Features/DecompilerDependent/README.md

@@ -0,0 +1 @@
+# DecompilerDependent

Ghidra/Features/DecompilerDependent/certification.manifest

@@ -1,5 +1,6 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 data/decompiler.dependent.theme.properties||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||||END|

Ghidra/Features/FileFormats/README.md

@@ -0,0 +1 @@
+# FileFormats

Ghidra/Features/FileFormats/certification.manifest

@@ -10,6 +10,7 @@
 ##MODULE IP: LGPL 2.1
 ##MODULE IP: Public Domain
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 data/android/eclipse-classpath||GHIDRA||reviewed||END|
 data/android/eclipse-project||GHIDRA||reviewed||END|

Ghidra/Features/FunctionGraph/README.md

@@ -0,0 +1 @@
+# FunctionGraph

Ghidra/Features/FunctionGraph/certification.manifest

@@ -4,6 +4,7 @@
 ##MODULE IP: Oxygen Icons - LGPL 3.0
 ##MODULE IP: Tango Icons - Public Domain
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/ExtensionPoint.manifest||GHIDRA||||END|
 data/functiongraph.theme.properties||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||||END|

Ghidra/Features/FunctionGraphDecompilerExtension/README.md

@@ -0,0 +1 @@
+# FunctionGraphDecompilerExtension

Ghidra/Features/FunctionGraphDecompilerExtension/certification.manifest

@@ -1,4 +1,5 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/functiongraph.extension.decompiler.theme.properties||GHIDRA||||END|
 src/main/resources/images/function_graph_code_flow.png||GHIDRA||reviewed||END|

Ghidra/Features/FunctionID/README.md

@@ -0,0 +1 @@
+# FunctionID

Ghidra/Features/FunctionID/certification.manifest

@@ -1,6 +1,7 @@
 ##VERSION: 2.0
 ##MODULE IP: Nuvola Icons - LGPL 2.1
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/building_fid.txt||GHIDRA||||END|
 data/common_symbols_win32.txt||GHIDRA|||Symbols used to generate fiddb files distributed with Ghidra|END|
 data/common_symbols_win64.txt||GHIDRA|||Symbols used to generate fiddb files distributed with Ghidra|END|

Ghidra/Features/GhidraGo/README.md

@@ -0,0 +1 @@
+# GhidraGo

Ghidra/Features/GhidraGo/certification.manifest

@@ -1,4 +1,5 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||||END|
 src/main/help/help/topics/GhidraGo/GhidraGo.html||GHIDRA||||END|

Ghidra/Features/GhidraServer/README.md

@@ -0,0 +1 @@
+# GhidraServer

Ghidra/Features/GhidraServer/certification.manifest

@@ -3,6 +3,7 @@
 ##MODULE IP: LGPL 2.1
 ##MODULE IP: Tango Icons - Public Domain
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/serial.filter||GHIDRA||||END|
 os/readme.txt||GHIDRA||||END|
 src/main/java/ghidra/server/remote/ServerHelp.txt||GHIDRA||||END|

Ghidra/Features/GnuDemangler/README.md

@@ -0,0 +1 @@
+# GnuDemangler

Ghidra/Features/GnuDemangler/certification.manifest

@@ -1,4 +1,5 @@
 ##VERSION: 2.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/default.gnu.demangler.replacements.txt||GHIDRA||||END|
 src/test/resources/ghidra/app/util/demangler/gnu_mangled_names.txt||GHIDRA||reviewed||END|

Ghidra/Features/GraphFunctionCalls/README.md

@@ -0,0 +1 @@
+# GraphFunctionCalls

Ghidra/Features/GraphFunctionCalls/certification.manifest

@@ -1,6 +1,7 @@
 ##VERSION: 2.0
 ##MODULE IP: Oxygen Icons - LGPL 3.0
 Module.manifest||GHIDRA||||END|
+README.md||GHIDRA||||END|
 data/functioncallgraph.theme.properties||GHIDRA||||END|
 src/main/help/help/TOC_Source.xml||GHIDRA||||END|
 src/main/help/help/topics/FunctionCallGraphPlugin/Function_Call_Graph.html||GHIDRA||||END|

Ghidra/Features/GraphServices/README.md

@@ -0,0 +1 @@
+# GraphServices