start talking about theseus

0_preamble/notations.typ

@@ -1,4 +1,7 @@
-#let tldr = link(<acr-tldr>)[TL;DR]
+#let APK = link(<acr-apk>)[APK]
+#let DEX = link(<acr-dex>)[DEX]
+#let OAT = link(<acr-oat>)[OAT]
+#let JAR = link(<acr-jar>)[JAR]
 
 #let notation_table = align(center, table(
   columns: 2,
@@ -6,5 +9,8 @@
   table.header(
     [Acronyms], [Meanings],
   ),
-  tldr, [Too long; didn't read<acr-tldr>],
+  APK, [Android Package, the file format used to install application on Android. The APK format is an extention of the #JAR format <acr-apk>],
+  DEX, [Dalvik Executable, the file format for the bytecode used for applicatiobs by Android <acr-dex>],
+  JAR, [Java ARchive file, the file format used to store several java class files. Sometimes used by Android to store #DEX files instead of java classes <acr-jar>],
+  OAT, [Of Ahead Time, an ahead of time compiled format for #DEX files <acr-oat>]
 ))

6_theseus/1_static_transformation.typ

@@ -0,0 +1,93 @@
+#import "../lib.typ": todo, APK, DEX, JAR, OAT, eg
+
+== Code Transformation <sec:th-trans>
+
+#todo[Define code loading and reflection somewhere]
+#todo[This is a draft, clean this up]
+#todo[Reflectif call? Reflection call?]
+
+In this section, we will see how we can transform the application code to make dynamic codeloading and reflexif calls analysable by static analysis tools.
+
+=== Reflection <sec:th-trans-ref>
+
+In Android, reflection can be used to do two things: instanciate a class, or call a method. 
+Either way, reflection starts by retreiving the `Class` object representing the class to use.
+This class is usually retrived using a `ClassLoader` object, but can also be retrieved directly from the classloader of the class defining the calling method.
+// elaborate? const-class dalvik instruction / MyClass.class in java?
+One the class is retrieve, it can be instanciated using the deprecated method `Class.newInstance()`, like shown in @lst:-th-expl-cl-new-instance, or a specific method can be retrieved.
+The current approche to instanciate a class is to retrieve the specific `Constructor` object, then calling `Constructor.newInstance(..)` like in @lst:-th-expl-cl-cnstr.
+Similarly, to call a method, the `Method` object must be retrieved, then called using `Method.invoke(..)`, like shown in @lst:-th-expl-cl-call.
+
+Although the process seems to differ between class instanciation and method call from the Java stand point, the runtime opperations are very similar.
+When instanciating an object with `Object obj = cst.newInstance("Hello Void")`, the constructor method `<init>(Ljava/lang/String;)V`, represented by the `Constructor` `cst`, is called on the object `obj`.
+
+#figure(
+  ```java
+  ClassLoader cl = MainActivity.class.getClassLoader();
+  Class clz = cl.loadClass("com.example.Reflectee");
+  Object obj = clz.newInstance();
+  ```,
+  caption: [Instanciating a class using `Class.newInstance()`]
+) <lst:-th-expl-cl-new-instance>
+
+#figure(
+  ```java
+  Constructor cst = clz.getDeclaredConstructor(String.class);
+  Object obj = cst.newInstance("Hello Void");
+  ```,
+  caption: [Instanciating a class using `Constructor.newInstance(..)`]
+) <lst:-th-expl-cl-cnstr>
+
+#figure(
+  ```java
+  Method mth = clz.getMethod("myMethod", String.class);
+  String retData = (String) mth.invoke(obj, "an argument");
+  ```,
+  caption: [Calling a method using reflection]
+) <lst:-th-expl-cl-call>
+
+To allow static analysis tools to analyse an application that use reflection, we want to replace the reflection call by the bytecode that does the actual calls.
+
+One of the main reason to use reflection is to access classes not from the application. 
+Although allows the use classes that do not exist in the application in bytecode, at runtime, if the classes are not found in the current classloader, the application will crash.
+Similarly, some analysis tools might have trouble analysis application calling non existing classes. 
+@sec:th-trans-cl deals with the issue of adding dynamically loaded bytecode to the application.
+
+A notable issue is that a specific reflection call can call different methods.
+@lst:th-worst-case-ref illustrate a worst case scenario where any method can be call at the same reflection call.
+In those situation, we cannot garanty that we know all the methodes that can be called (#eg the name of the method called could be retrieved from a remote server).
+
+
+#figure(
+  ```java
+  Object myInvoke(Object obj, Method mth, Object[] args) throws .. {
+    return mth.invoke(obj, args);
+  }
+  ```,
+  caption: [A reflection call that can call any method]
+) <lst:th-worst-case-ref>
+
+=== Code loading <sec:th-trans-cl>
+
+#todo[custom class loaders]
+
+An application can dynamically import code from several format like #DEX, #APK, #JAR or #OAT, either stored in memory or in a file.
+Because it is an internal, platform dependant format, we elected to ignore the #OAT format.
+Practically, #JAR and #APK files are zip files containing #DEX files.
+This means that we only need to find a way to integrate #DEX files to the application.
+
+We elected to simply add the dex files to the application, using the multi-dex feature introduced by the SDK 21 now used by all applications.
+This gives access to the dynamically loaded code to static analysis tool. 
+
+#todo[add drawing of dex insertion]
+
+We decided to leave untouched the original code that load the bytecode.
+At runtime, although the bytecode is already present in the application, the application will still dynamically load the code.
+This ensure that the application keep working as intended even if the transformation we applied are incomplete.
+Specifically, to call dynamically loaded code, an application needs to use reflection, and we saw in @sec:th-trans-ref that we need to keep reflecton calls, and in order to keep reflection calls, we need the classloader created when loading bytecode.
+
+=== Class Collisions <sec:th-class-collision>
+
+=== Pitfalls
+
+#todo[interupting try blocks: catch block might expect temporary registers to still stored the saved value]

6_theseus/3_results.typ

@@ -0,0 +1,7 @@
+#import "../lib.typ": todo
+
+== Results #todo[better section name] <sec:th-res>
+
+=== Bytecode Loaded by Application <sec:th-code-collected>
+
+#todo[Bytecode collected: facebook, google, appsflyer]

6_theseus/4_ttv.typ

@@ -0,0 +1,9 @@
+#import "../lib.typ": todo
+
+== Limits and Threat to Validity <sec-ttv>
+
+#todo[redaction]
+
+- Use multidex: min SDK >= 21 (android 5.0, published in 2014, should be ok)
+- No support for OAT (platform dependent)
+

6_theseus/main.typ

@@ -0,0 +1,7 @@
+#import "../lib.typ": todo
+
+= #todo[theseus chapter title]
+
+#include("1_static_transformation.typ")
+#include("3_results.typ")
+#include("4_ttv.typ")

lib.typ

@@ -1,4 +1,6 @@
 #import "@local/template-thesis-matisse:0.0.1": *
+// Notations:
+#import "0_preamble/notations.typ": *
 
 // Format number.
 // Following https://www.mit.edu/course/21/21.guide/numbers.htm

main.typ

@@ -74,10 +74,7 @@
 #include("3_related_work/main.typ")
 #include("4_rasta/main.typ")
 #include("5_class_loader/main.typ")
-
+#include("6_theseus/main.typ")
-= Contribution n
-
-#lorem(500)
 
 = Conclusion <sec:conclusion>