diff --git a/CMakeLists.txt b/CMakeLists.txt
index 124c624..6e3a3e3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -209,6 +209,11 @@ endforeach()
 
 # -----------------------------------------------------------------------------
 
+find_program(IWYU NAMES include-what-you-use iwyu REQUIRED)
+set_property(TARGET factgen-exe PROPERTY CXX_INCLUDE_WHAT_YOU_USE ${IWYU})
+
+# -----------------------------------------------------------------------------
+
 if(NOT (DEFINED CLANG_VERSION))
   set(CLANG_VERSION ${LLVM_MAJOR_VERSION})
 endif()
diff --git a/FactGenerator/include/FactGenerator.hpp b/FactGenerator/include/FactGenerator.hpp
index 62f66fd..bae56d6 100644
--- a/FactGenerator/include/FactGenerator.hpp
+++ b/FactGenerator/include/FactGenerator.hpp
@@ -1,32 +1,50 @@
 #ifndef CSV_GENERATOR_H__
 #define CSV_GENERATOR_H__
 
-#include <llvm/IR/Constants.h>
-#include <llvm/IR/DataLayout.h>
-#include <llvm/IR/GlobalValue.h>
-#include <llvm/IR/GlobalVariable.h>
-#include <llvm/IR/InlineAsm.h>
-#include <llvm/IR/Type.h>
-#include <llvm/IR/Value.h>
-#include <llvm/Support/raw_ostream.h>
-
-#include <boost/flyweight.hpp>
-#include <boost/unordered_map.hpp>
-#include <boost/unordered_set.hpp>
-#include <set>
-#include <string>
-
-#include "ContextSensitivity.hpp"
-#include "Demangler.hpp"
-#include "FactWriter.hpp"
-#include "ForwardingFactWriter.hpp"
-#include "RefmodeEngine.hpp"
-#include "Signatures.hpp"
-#include "predicate_groups.hpp"
-
+#include <llvm/ADT/Optional.h>  // for Optional
+#include <llvm/Support/JSON.h>  // IWYU pragma: keep
+
+#include <boost/container_hash/extensions.hpp>  // for hash
+#include <boost/filesystem/path.hpp>            // for path
+#include <boost/flyweight/flyweight.hpp>        // for flyweight
+#include <boost/unordered/unordered_map.hpp>    // for unordered_map
+#include <boost/unordered/unordered_set.hpp>    // for unordered_set
+#include <map>                                  // for map
+#include <regex>                                // for regex
+#include <string>                               // for string, basic_string
+#include <tuple>                                // for tuple
+#include <vector>                               // for vector
+
+#include "ContextSensitivity.hpp"    // for ContextSensitivity
+#include "Demangler.hpp"             // for Demangler
+#include "ForwardingFactWriter.hpp"  // for ForwardingFactWriter
+#include "RefmodeEngine.hpp"         // for refmode_t, RefmodeEngine
+#include "predicate_groups.hpp"      // for pred_t
+
+// Forward declarations
 namespace cclyzer {
-class FactGenerator;
+class FactWriter;
 }
+namespace llvm {
+class Constant;
+class ConstantArray;
+class ConstantExpr;
+class ConstantStruct;
+class ConstantVector;
+class DataLayout;
+class Function;
+class GlobalAlias;
+class GlobalVariable;
+class InlineAsm;
+class Module;
+class NamedMDNode;
+class Type;
+class Value;
+}  // namespace llvm
+
+namespace cclyzer {
+class FactGenerator;  // IWYU pragma: keep
+}  // namespace cclyzer
 
 class cclyzer::FactGenerator : private RefmodeEngine,
                                private Demangler,
diff --git a/FactGenerator/include/FactWriter.hpp b/FactGenerator/include/FactWriter.hpp
index 270ef6f..ea76c99 100644
--- a/FactGenerator/include/FactWriter.hpp
+++ b/FactGenerator/include/FactWriter.hpp
@@ -1,16 +1,17 @@
 #ifndef FACT_WRITER_H__
 #define FACT_WRITER_H__
 
-#include <boost/filesystem.hpp>
-#include <boost/unordered_map.hpp>
-#include <string>
+// IWYU pragma: no_include "boost/unordered/detail/implementation.hpp"
+#include <boost/filesystem/path.hpp>          // for path
+#include <boost/unordered/unordered_map.hpp>  // for unordered_map
+#include <string>                             // for string
 
-#include "RefmodeEngine.hpp"  // TODO replace
-#include "csv_writer.hpp"
-#include "predicate.hpp"
+#include "RefmodeEngine.hpp"  // for refmode_t
+#include "csv_writer.hpp"     // for csv_writer
+#include "predicate.hpp"      // for Predicate
 
 namespace cclyzer {
-class FactWriter;
+class FactWriter;  // IWYU pragma: keep
 }
 
 class cclyzer::FactWriter {
diff --git a/FactGenerator/include/InstructionVisitor.hpp b/FactGenerator/include/InstructionVisitor.hpp
index 73d9a92..0e85284 100644
--- a/FactGenerator/include/InstructionVisitor.hpp
+++ b/FactGenerator/include/InstructionVisitor.hpp
@@ -1,17 +1,25 @@
 #ifndef INSTR_VISITOR_H__
 #define INSTR_VISITOR_H__
 
-#include <llvm/IR/InstVisitor.h>
-
-#include <string>
-
-#include "FactGenerator.hpp"
-#include "RefmodeEngine.hpp"
-
-// Add to namespace
-namespace cclyzer {
-class InstructionVisitor;
-}
+#include <llvm/IR/InstVisitor.h>          // for InstVisitor
+#include <llvm/IR/InstrTypes.h>           // for CastInst, BinaryOperator
+#include <llvm/IR/Instructions.h>         // for AllocaInst (ptr only), Atom...
+#include <llvm/IR/LLVMContext.h>          // for SingleThread
+#include <llvm/Support/AtomicOrdering.h>  // for AtomicOrdering
+#include <llvm/Support/ErrorHandling.h>   // for llvm
+
+#include "FactGenerator.hpp"     // for FactGenerator
+#include "RefmodeEngine.hpp"     // for refmode_t
+#include "predicate_groups.hpp"  // for instr, instr::flag
+
+// Forward declares
+namespace llvm {
+class DbgDeclareInst;
+class Instruction;
+class Module;
+class User;
+class Value;
+}  // namespace llvm
 
 // Processor of instructions
 class cclyzer::InstructionVisitor
diff --git a/FactGenerator/include/Options.hpp b/FactGenerator/include/Options.hpp
index 0fca671..aacf795 100644
--- a/FactGenerator/include/Options.hpp
+++ b/FactGenerator/include/Options.hpp
@@ -1,15 +1,17 @@
 #ifndef OPTIONS_HPP__
 #define OPTIONS_HPP__
 
-#include <llvm/ADT/Optional.h>
+#include <llvm/ADT/Optional.h>  // for Optional
 
-#include <boost/filesystem.hpp>
-#include <string>
+#include <algorithm>                  // for max
+#include <boost/filesystem/path.hpp>  // for path
+#include <string>                     // for string
+#include <vector>                     // for vector
 
-#include "ContextSensitivity.hpp"
+#include "ContextSensitivity.hpp"  // for ContextSensitivity
 
 namespace cclyzer {
-class Options;
+class Options;  // IWYU pragma: keep
 }
 
 class cclyzer::Options {
diff --git a/FactGenerator/include/RefmodeEngine.hpp b/FactGenerator/include/RefmodeEngine.hpp
index a3a4ea7..795cd4e 100644
--- a/FactGenerator/include/RefmodeEngine.hpp
+++ b/FactGenerator/include/RefmodeEngine.hpp
@@ -1,18 +1,20 @@
 #ifndef REFMODE_ENGINE_HPP__
 #define REFMODE_ENGINE_HPP__
 
-#include <llvm/IR/CallingConv.h>
-#include <llvm/IR/Function.h>
-#include <llvm/IR/GlobalValue.h>
-#include <llvm/IR/GlobalVariable.h>
-#include <llvm/IR/Instructions.h>
-#include <llvm/IR/Module.h>
-#include <llvm/IR/Type.h>
-#include <llvm/IR/Value.h>
-
-#include <boost/flyweight.hpp>
+#include <llvm/IR/CallingConv.h>     // IWYU pragma: keep
+#include <llvm/IR/GlobalValue.h>     // IWYU pragma: keep
+#include <llvm/IR/GlobalVariable.h>  // IWYU pragma: keep
+#include <llvm/IR/Instructions.h>    // IWYU pragma: keep
+
+#include <boost/flyweight.hpp>  // IWYU pragma: keep
 #include <string>
 
+namespace llvm {
+class Function;
+class Module;
+class Value;
+}  // namespace llvm
+
 namespace cclyzer {
 
 namespace refmode {
diff --git a/FactGenerator/include/TypeAccumulator.hpp b/FactGenerator/include/TypeAccumulator.hpp
index 6c1b835..a8c8b0d 100644
--- a/FactGenerator/include/TypeAccumulator.hpp
+++ b/FactGenerator/include/TypeAccumulator.hpp
@@ -1,14 +1,18 @@
 #ifndef TYPE_ACCUMULATOR_HPP__
 #define TYPE_ACCUMULATOR_HPP__
 
-#include <llvm/IR/DerivedTypes.h>
-#include <llvm/IR/Type.h>
-#include <llvm/Support/raw_ostream.h>
+#include <llvm/Config/llvm-config.h>   // for LLVM_VERSION_MAJOR
+#include <llvm/IR/DerivedTypes.h>      // for StructType, FunctionType
+#include <llvm/IR/Type.h>              // for Type
+#include <llvm/Support/Casting.h>      // for cast, dyn_cast
+#include <llvm/Support/raw_ostream.h>  // for errs, raw_fd_ostream
+#include <stddef.h>                    // for size_t
 
-#include <boost/unordered_set.hpp>
+#include <boost/container_hash/extensions.hpp>  // for hash
+#include <boost/unordered/unordered_set.hpp>    // for unordered_set
 
 namespace cclyzer::llvm_utils {
-class TypeAccumulator;
+class TypeAccumulator;  // IWYU pragma: keep
 }  // namespace cclyzer::llvm_utils
 
 class cclyzer::llvm_utils::TypeAccumulator {
diff --git a/FactGenerator/include/TypeVisitor.hpp b/FactGenerator/include/TypeVisitor.hpp
index 39be766..446ba87 100644
--- a/FactGenerator/include/TypeVisitor.hpp
+++ b/FactGenerator/include/TypeVisitor.hpp
@@ -1,6 +1,13 @@
-#include <llvm/IR/DataLayout.h>
-#include <llvm/IR/DerivedTypes.h>
-#include <llvm/IR/Type.h>
+// Forward decls
+namespace llvm {
+class ArrayType;
+class DataLayout;
+class FunctionType;
+class PointerType;
+class StructType;
+class Type;
+class VectorType;
+}  // namespace llvm
 
 namespace cclyzer {
 // Forward declaration
diff --git a/FactGenerator/include/llvm_enums.hpp b/FactGenerator/include/llvm_enums.hpp
index 4e5660c..2645c91 100644
--- a/FactGenerator/include/llvm_enums.hpp
+++ b/FactGenerator/include/llvm_enums.hpp
@@ -1,12 +1,12 @@
 #ifndef LLVM_ENUMS_HPP__
 #define LLVM_ENUMS_HPP__
 
-#include <llvm/IR/CallingConv.h>
-#include <llvm/IR/GlobalValue.h>
-#include <llvm/IR/GlobalVariable.h>
-#include <llvm/IR/Instructions.h>
+#include <llvm/IR/CallingConv.h>          // for ID
+#include <llvm/IR/GlobalValue.h>          // for GlobalValue, GlobalValue::L...
+#include <llvm/IR/GlobalVariable.h>       // for GlobalVariable
+#include <llvm/Support/AtomicOrdering.h>  // for AtomicOrdering
 
-#include <string>
+#include <string>  // for string
 
 namespace cclyzer::utils {
 // Functions that convert the various LLVM enums to strings
diff --git a/FactGenerator/include/predicate.hpp b/FactGenerator/include/predicate.hpp
index e6c7a5d..891bac9 100644
--- a/FactGenerator/include/predicate.hpp
+++ b/FactGenerator/include/predicate.hpp
@@ -1,13 +1,11 @@
 #ifndef PREDICATE_H__
 #define PREDICATE_H__
 
-#include <memory>
+#include <iosfwd>
 #include <set>
 #include <string>
 #include <utility>
 
-#include "Singleton.hpp"
-
 namespace cclyzer {
 /* Forward declarations to be able to define actual registries */
 class Predicate;
diff --git a/FactGenerator/src/FactGenerator.cpp b/FactGenerator/src/FactGenerator.cpp
index 7a5e48b..409af5f 100644
--- a/FactGenerator/src/FactGenerator.cpp
+++ b/FactGenerator/src/FactGenerator.cpp
@@ -1,17 +1,41 @@
 #include "FactGenerator.hpp"
 
-#include <llvm/IR/CFG.h>
-#include <llvm/IR/Constants.h>
-#include <llvm/IR/Module.h>
-#include <llvm/IR/Operator.h>
-
-#include <regex>
-#include <string>
-
-#include "ContextSensitivity.hpp"
-#include "InstructionVisitor.hpp"
-#include "Signatures.hpp"
-#include "predicate_groups.hpp"
+#include <llvm/ADT/SmallVector.h>     // for SmallVector, SmallVectorTemplat...
+#include <llvm/ADT/StringRef.h>       // for StringRef
+#include <llvm/ADT/ilist_iterator.h>  // for operator!=, ilist_iterator
+#include <llvm/IR/BasicBlock.h>       // for BasicBlock
+#include <llvm/IR/CFG.h>              // for const_pred_iterator, pred_begin
+#include <llvm/IR/DebugLoc.h>         // for DebugLoc
+#include <llvm/IR/Function.h>         // for Function
+#include <llvm/IR/GlobalAlias.h>      // for GlobalAlias
+#include <llvm/IR/GlobalVariable.h>   // for GlobalVariable
+#include <llvm/IR/Instruction.h>      // for Instruction
+#include <llvm/IR/Metadata.h>         // for MDNode (ptr only), NamedMDNode
+#include <llvm/IR/Module.h>           // for Module, Module::const_alias_ite...
+#include <llvm/IR/Type.h>             // for Type
+#include <llvm/Support/Casting.h>     // for cast, isa
+#include <llvm/Support/JSON.h>        // for Array
+#include <stddef.h>                   // for size_t
+
+#include <RefmodeEngine.hpp>    // for refmode_t
+#include <boost/operators.hpp>  // for operator++
+#include <regex>                // for regex, regex_search, match_resu...
+#include <string>               // for string, operator==, basic_string
+#include <utility>              // for pair
+
+#include "ContextSensitivity.hpp"  // for context_sensitivity_to_string
+#include "InstructionVisitor.hpp"  // for InstructionVisitor
+#include "Signatures.hpp"          // for emit_signatures, preprocess_sig...
+#include "predicate_groups.hpp"    // for instr, variable, block, block::...
+
+// Forward declarations
+namespace cclyzer {
+class FactWriter;
+}
+namespace llvm {
+class GlobalValue;
+class Value;
+}  // namespace llvm
 
 using cclyzer::FactGenerator;
 using llvm::cast;
diff --git a/FactGenerator/src/FactWriter.cpp b/FactGenerator/src/FactWriter.cpp
index 32baf47..5a2a680 100644
--- a/FactGenerator/src/FactWriter.cpp
+++ b/FactGenerator/src/FactWriter.cpp
@@ -1,7 +1,13 @@
+// IWYU pragma: no_include <boost/unordered/detail/implementation.hpp>
 #include "FactWriter.hpp"
 
 #include <algorithm>
+#include <boost/filesystem/operations.hpp>   // for create_directory
+#include <boost/filesystem/path_traits.hpp>  // for filesystem
+#include <map>                               // for operator!=, _Rb...
+#include <utility>                           // for move
 
+#include "csv_writer.hpp"  // for csv_writer
 #include "predicate_groups.hpp"
 
 namespace fs = boost::filesystem;
diff --git a/FactGenerator/src/InstructionVisitor.cpp b/FactGenerator/src/InstructionVisitor.cpp
index 6868592..5f9c571 100644
--- a/FactGenerator/src/InstructionVisitor.cpp
+++ b/FactGenerator/src/InstructionVisitor.cpp
@@ -1,12 +1,36 @@
 #include "InstructionVisitor.hpp"
 
-#include <llvm/IR/DebugInfo.h>
-#include <llvm/IR/Operator.h>
-
-#include <cassert>
-#include <string>
-
-#include "predicate_groups.hpp"
+#include <llvm/ADT/APInt.h>             // for APInt
+#include <llvm/ADT/SmallString.h>       // for SmallString
+#include <llvm/ADT/StringRef.h>         // for StringRef
+#include <llvm/ADT/iterator.h>          // for iterator_facade_base
+#include <llvm/ADT/iterator_range.h>    // for iterator_range
+#include <llvm/Config/llvm-config.h>    // for LLVM_VERSION_MAJOR
+#include <llvm/IR/BasicBlock.h>         // for BasicBlock
+#include <llvm/IR/CallingConv.h>        // for C
+#include <llvm/IR/Constant.h>           // for Constant
+#include <llvm/IR/Constants.h>          // for UndefValue, ConstantInt
+#include <llvm/IR/DebugInfoMetadata.h>  // for DILocalVariable
+#include <llvm/IR/DebugLoc.h>           // for DebugLoc
+#include <llvm/IR/Instruction.h>        // for Instruction
+#include <llvm/IR/IntrinsicInst.h>      // for DbgDeclareInst
+#include <llvm/IR/Operator.h>           // for FPMathOperator, OverflowingBi...
+#include <llvm/IR/User.h>               // for User
+#include <llvm/IR/Value.h>              // for Value
+#include <llvm/Support/Casting.h>       // for dyn_cast, isa
+#include <llvm/Support/raw_ostream.h>   // for errs, raw_ostream, raw_fd_ost...
+
+#include <FactGenerator.hpp>  // for FactGenerator
+#include <RefmodeEngine.hpp>  // for refmode_t
+#include <string>             // for string, basic_string
+
+#include "predicate_groups.hpp"  // for instr, instr::flag, br, cmpxchg
+namespace llvm {
+class InlineAsm;
+}
+namespace llvm {
+class Type;
+}
 
 namespace pred = cclyzer::predicates;
 
diff --git a/FactGenerator/src/Options.cpp b/FactGenerator/src/Options.cpp
index 99a9e9f..31b6f0a 100644
--- a/FactGenerator/src/Options.cpp
+++ b/FactGenerator/src/Options.cpp
@@ -1,12 +1,31 @@
 #include "Options.hpp"
 
-#include <boost/filesystem.hpp>
-#include <boost/program_options.hpp>
+#include <stdlib.h>  // for exit, EXI...
+
+// IWYU pragma: no_include <boost/detail/basic_pointerbuf.hpp>
+// IWYU pragma: no_include <boost/program_options/detail/parsers.hpp>
+// IWYU pragma: no_include <boost/program_options/detail/value_semantic.hpp>
+#include <ContextSensitivity.hpp>                   // for ContextSe...
+#include <boost/filesystem.hpp>                     // IWYU pragma: keep
+#include <boost/filesystem/convenience.hpp>         // for basename
+#include <boost/filesystem/directory.hpp>           // for directory...
+#include <boost/filesystem/operations.hpp>          // for exists
+#include <boost/filesystem/path_traits.hpp>         // for filesystem
+#include <boost/iterator/iterator_facade.hpp>       // for operator!=
+#include <boost/lexical_cast/bad_lexical_cast.hpp>  // for bad_lexic...
+#include <boost/program_options.hpp>                // IWYU pragma: keep
+#include <boost/program_options/errors.hpp>         // for required_...
 #include <boost/program_options/options_description.hpp>
 #include <boost/program_options/parsers.hpp>
+#include <boost/program_options/positional_options.hpp>  // for positiona...
+#include <boost/program_options/value_semantic.hpp>      // for typed_value
 #include <boost/program_options/variables_map.hpp>
+#include <boost/range/iterator_range_core.hpp>     // for iterator_...
+#include <boost/type_index/type_index_facade.hpp>  // for operator==
 #include <cassert>
 #include <iostream>
+#include <sstream>  // for basic_str...
+#include <utility>
 
 namespace fs = boost::filesystem;
 namespace po = boost::program_options;
diff --git a/FactGenerator/src/RefmodeEngine.cpp b/FactGenerator/src/RefmodeEngine.cpp
index f51f650..109337c 100644
--- a/FactGenerator/src/RefmodeEngine.cpp
+++ b/FactGenerator/src/RefmodeEngine.cpp
@@ -1,14 +1,28 @@
 #include "RefmodeEngine.hpp"
 
-#include <llvm/IR/DebugInfoMetadata.h>
-#include <llvm/IR/InlineAsm.h>
-#include <llvm/Support/raw_ostream.h>
-
-#include <boost/flyweight.hpp>
-#include <sstream>
-
-#include "RefmodeEngineImpl.hpp"
-#include "llvm_enums.hpp"
+#include <llvm/IR/BasicBlock.h>         // for BasicBlock
+#include <llvm/IR/Constant.h>           // for Constant
+#include <llvm/IR/DebugInfoMetadata.h>  // for DINode
+#include <llvm/IR/DerivedTypes.h>       // for StructType
+#include <llvm/IR/Function.h>           // for Function
+#include <llvm/IR/GlobalValue.h>        // for GlobalValue
+#include <llvm/IR/Metadata.h>           // for MDNode
+#include <llvm/IR/Type.h>               // for Type
+#include <llvm/Support/Casting.h>       // for cast, dyn_cast, isa
+#include <llvm/Support/raw_ostream.h>   // for raw_string_ostream, raw_ostream
+
+#include <memory>   // for unique_ptr
+#include <sstream>  // for ostringstream, operator<<
+
+#include "ContextManager.hpp"     // for ContextManager
+#include "RefmodeEngineImpl.hpp"  // for RefmodeEngine::Impl
+#include "llvm_enums.hpp"         // for to_string, utils
+namespace llvm {
+class InlineAsm;
+}
+namespace llvm {
+class Instruction;
+}
 
 using cclyzer::refmode_t;
 using cclyzer::RefmodeEngine;
diff --git a/FactGenerator/src/RefmodeEngineImpl.cpp b/FactGenerator/src/RefmodeEngineImpl.cpp
index 7f6562b..7a3f76c 100644
--- a/FactGenerator/src/RefmodeEngineImpl.cpp
+++ b/FactGenerator/src/RefmodeEngineImpl.cpp
@@ -1,11 +1,24 @@
 #include "RefmodeEngineImpl.hpp"
 
-#include <llvm/IR/Metadata.h>
-#include <llvm/Support/raw_ostream.h>
-
-#include <boost/algorithm/string.hpp>
-#include <boost/flyweight.hpp>
-#include <map>
+#include <llvm/ADT/ilist_iterator.h>   // for ilist_iterator, operator!=
+#include <llvm/ADT/iterator_range.h>   // for iterator_range
+#include <llvm/IR/Argument.h>          // for Argument
+#include <llvm/IR/BasicBlock.h>        // for BasicBlock
+#include <llvm/IR/Instruction.h>       // for Instruction
+#include <llvm/IR/Metadata.h>          // for ValueAsMetadata, Metadata...
+#include <llvm/IR/Type.h>              // for Type
+#include <llvm/IR/Value.h>             // for Value
+#include <llvm/Support/raw_ostream.h>  // for raw_string_ostream, raw_o...
+
+#include <RefmodeEngine.hpp>                // for RefmodeEngine, refmode_t
+#include <boost/algorithm/string/trim.hpp>  // for trim
+#include <map>                              // for map
+
+// Forward decl
+namespace llvm {
+class Constant;
+class GlobalValue;
+}  // namespace llvm
 
 using cclyzer::refmode_t;
 using cclyzer::RefmodeEngine;
diff --git a/FactGenerator/src/RefmodeEngineImpl.hpp b/FactGenerator/src/RefmodeEngineImpl.hpp
index 55565ea..f5757bc 100644
--- a/FactGenerator/src/RefmodeEngineImpl.hpp
+++ b/FactGenerator/src/RefmodeEngineImpl.hpp
@@ -1,15 +1,24 @@
-#include <llvm/IR/ModuleSlotTracker.h>
+#include <assert.h>                     // for assert
+#include <llvm/IR/Function.h>           // for Function
+#include <llvm/IR/ModuleSlotTracker.h>  // for ModuleSlotTracker
+#include <llvm/Support/Casting.h>       // for isa, dyn_cast
 
-#include <memory>
-#include <sstream>
+#include <map>     // for map
+#include <memory>  // for unique_ptr, make_unique
+#include <string>  // for string
+#include <vector>  // for vector
 
-#include "ContextManager.hpp"
-#include "RefmodeEngine.hpp"
+#include "ContextManager.hpp"  // for ContextManager, ContextManage...
+#include "RefmodeEngine.hpp"   // for refmode_t, RefmodeEngine
 
 // Forward declaration
 namespace llvm {
+class BasicBlock;
+class Metadata;
+class Module;
+class Value;
 class raw_string_ostream;
-}
+}  // namespace llvm
 
 // Refmode Policy implementation
 class cclyzer::RefmodeEngine::Impl {
diff --git a/FactGenerator/src/Signatures.cpp b/FactGenerator/src/Signatures.cpp
index 050f620..edb4dec 100644
--- a/FactGenerator/src/Signatures.cpp
+++ b/FactGenerator/src/Signatures.cpp
@@ -1,4 +1,24 @@
-#include "Signatures.hpp"
+#include <llvm/ADT/DenseMap.h>   // for DenseMapPair, DenseMapIterator
+#include <llvm/ADT/Optional.h>   // for Optional
+#include <llvm/ADT/StringRef.h>  // for StringRef
+#include <llvm/Support/Error.h>  // for Expected
+#include <llvm/Support/JSON.h>   // for Array, Value, Object, parse, Obj...
+#include <stddef.h>              // for size_t
+
+#include <ForwardingFactWriter.hpp>   // for ForwardingFactWriter
+#include <boost/filesystem/path.hpp>  // for path
+#include <cstdint>                    // for int64_t
+#include <iterator>                   // for istreambuf_iterator, operator!=
+#include <map>                        // for map
+#include <regex>
+#include <sstream>      // for basic_stringbuf<>::int_type, bas...
+#include <stdexcept>    // for invalid_argument
+#include <string>       // for string, operator==, operator+
+#include <tuple>        // for tuple, get, make_tuple, tuple_cat
+#include <type_traits>  // for remove_reference_t
+#include <vector>       // for vector
+
+#include "predicate_groups.hpp"  // for signature, signature::arg_alloc
 
 template <typename T>
 auto extract_from_array(const llvm::json::Array &json_array, size_t index)
diff --git a/FactGenerator/src/TypeVisitor.cpp b/FactGenerator/src/TypeVisitor.cpp
index 6baa12d..fbb7fd2 100644
--- a/FactGenerator/src/TypeVisitor.cpp
+++ b/FactGenerator/src/TypeVisitor.cpp
@@ -1,7 +1,21 @@
 #include "TypeVisitor.hpp"
 
-#include "FactGenerator.hpp"
-#include "predicate_groups.hpp"
+#include <assert.h>                   // for assert
+#include <llvm/ADT/StringRef.h>       // for StringRef
+#include <llvm/Config/llvm-config.h>  // for LLVM_VERSION_MAJOR
+#include <llvm/IR/DataLayout.h>       // for DataLayout, StructLayout
+#include <llvm/IR/DerivedTypes.h>     // for StructType, FunctionType, Vecto...
+#include <llvm/IR/Type.h>             // for Type, Type::ArrayTyID, Type::BF...
+#include <llvm/Support/Casting.h>     // for cast, isa
+#include <llvm/Support/TypeSize.h>    // for TypeSize
+#include <stddef.h>                   // for size_t
+#include <stdint.h>                   // for uint64_t
+
+#include <RefmodeEngine.hpp>  // for refmode_t
+#include <string>             // for basic_string
+
+#include "FactGenerator.hpp"     // for FactGenerator
+#include "predicate_groups.hpp"  // for struct_type, func_type, array_type
 
 using cclyzer::TypeVisitor;
 namespace pred = cclyzer::predicates;
diff --git a/FactGenerator/src/assembly.cpp b/FactGenerator/src/assembly.cpp
index e1184dd..c8978e5 100644
--- a/FactGenerator/src/assembly.cpp
+++ b/FactGenerator/src/assembly.cpp
@@ -1,11 +1,23 @@
-#include <llvm/IR/InlineAsm.h>
-
-#include <boost/algorithm/string/replace.hpp>
-#include <boost/functional/hash.hpp>
-#include <string>
-
-#include "FactGenerator.hpp"
-#include "predicate_groups.hpp"
+#include <llvm/IR/DerivedTypes.h>        // for PointerType
+#include <llvm/IR/InlineAsm.h>           // for InlineAsm
+#include <llvm/Support/Casting.h>        // for cast, isa
+#include <llvm/Support/ErrorHandling.h>  // for llvm
+#include <stddef.h>                      // for size_t
+
+#include <RefmodeEngine.hpp>                    // for refmode_t
+#include <boost/algorithm/string/replace.hpp>   // for replace_all
+#include <boost/container_hash/extensions.hpp>  // for hash
+#include <boost/iterator/iterator_traits.hpp>   // for iterator_value<>::type
+#include <boost/unordered/unordered_set.hpp>    // for unordered_set
+#include <deque>                                // for _Deque_iterator
+#include <string>                               // for string, allocator
+
+#include "FactGenerator.hpp"     // for FactGenerator
+#include "predicate_groups.hpp"  // for constant, inline_asm
+
+namespace llvm {
+class Type;
+}
 
 using cclyzer::FactGenerator;
 using llvm::cast;
diff --git a/FactGenerator/src/constants.cpp b/FactGenerator/src/constants.cpp
index 07454d5..2345b17 100644
--- a/FactGenerator/src/constants.cpp
+++ b/FactGenerator/src/constants.cpp
@@ -1,9 +1,25 @@
+#include <llvm/ADT/APInt.h>           // for APInt
+#include <llvm/ADT/SmallString.h>     // for SmallString
+#include <llvm/ADT/StringRef.h>       // for StringRef
+#include <llvm/Config/llvm-config.h>  // for LLVM_VERSION_MAJOR
+#include <llvm/IR/Constant.h>         // for Constant
 #include <llvm/IR/Constants.h>
-
-#include <boost/functional/hash.hpp>
+#include <llvm/IR/Function.h>          // for Function
+#include <llvm/IR/GlobalVariable.h>    // for GlobalVariable
+#include <llvm/Support/Casting.h>      // for isa, cast
+#include <llvm/Support/MathExtras.h>   // for llvm
+#include <llvm/Support/raw_ostream.h>  // for raw_string_ostream
+#include <stddef.h>                    // for size_t
+
+#include <RefmodeEngine.hpp>                    // for refmode_t
+#include <boost/container_hash/extensions.hpp>  // for hash
+#include <boost/flyweight/flyweight.hpp>        // for flyweight, operator<
+#include <boost/operators.hpp>                  // for operator++
+#include <map>                                  // for map
 #include <string>
 
 #include "FactGenerator.hpp"
+#include "llvm/IR/Instruction.h"  // for Instruction::BitCast
 #include "predicate_groups.hpp"
 
 using cclyzer::FactGenerator;
diff --git a/FactGenerator/src/functions.cpp b/FactGenerator/src/functions.cpp
index e378b4e..1e7dbb5 100644
--- a/FactGenerator/src/functions.cpp
+++ b/FactGenerator/src/functions.cpp
@@ -1,9 +1,22 @@
-#include <llvm/Config/llvm-config.h>
-#include <llvm/IR/Constants.h>
-#include <llvm/IR/Function.h>
-
-#include "FactGenerator.hpp"
-#include "predicate_groups.hpp"
+#include <llvm/ADT/StringRef.h>       // for StringRef
+#include <llvm/Config/llvm-config.h>  // for LLVM_VERSION_MAJOR, LLVM_VE...
+#include <llvm/IR/Argument.h>         // for Argument
+#include <llvm/IR/CallingConv.h>      // for C
+#include <llvm/IR/DerivedTypes.h>     // for FunctionType
+#include <llvm/IR/Function.h>         // for Function, Function::const_a...
+
+#include <RefmodeEngine.hpp>              // for refmode_t
+#include <boost/flyweight/flyweight.hpp>  // for flyweight, operator<
+#include <boost/operators.hpp>            // for operator++
+#include <map>                            // for map
+#include <string>                         // for string, operator==, operator+
+
+#include "FactGenerator.hpp"     // for FactGenerator
+#include "predicate_groups.hpp"  // for func, func::alignment, func...
+namespace llvm {
+class Constant;
+class Value;
+}  // namespace llvm
 
 using cclyzer::FactGenerator;
 namespace pred = cclyzer::predicates;
diff --git a/FactGenerator/src/globals.cpp b/FactGenerator/src/globals.cpp
index bd913dd..8ba0e59 100644
--- a/FactGenerator/src/globals.cpp
+++ b/FactGenerator/src/globals.cpp
@@ -1,8 +1,20 @@
-#include <llvm/Config/llvm-config.h>
-#include <llvm/IR/Constants.h>
-
-#include "FactGenerator.hpp"
-#include "predicate_groups.hpp"
+#include <llvm/ADT/StringRef.h>       // for StringRef
+#include <llvm/Config/llvm-config.h>  // for LLVM_VERSION_MAJOR, LLVM_VE...
+#include <llvm/IR/DerivedTypes.h>     // for PointerType
+#include <llvm/IR/GlobalAlias.h>      // for GlobalAlias
+#include <llvm/IR/GlobalVariable.h>   // for GlobalVariable
+
+#include <RefmodeEngine.hpp>              // for refmode_t
+#include <boost/flyweight/flyweight.hpp>  // for flyweight, operator<
+#include <boost/operators.hpp>            // for operator++
+#include <map>                            // for map
+#include <string>                         // for string, operator==, operator+
+
+#include "FactGenerator.hpp"     // for FactGenerator
+#include "predicate_groups.hpp"  // for global_var, alias, global_v...
+namespace llvm {
+class Constant;
+}
 
 using cclyzer::FactGenerator;
 namespace pred = cclyzer::predicates;
diff --git a/FactGenerator/src/llvm_enums.cpp b/FactGenerator/src/llvm_enums.cpp
index 5de88d9..80a899a 100644
--- a/FactGenerator/src/llvm_enums.cpp
+++ b/FactGenerator/src/llvm_enums.cpp
@@ -1,8 +1,7 @@
 #include "llvm_enums.hpp"
 
-#include <llvm/Support/raw_ostream.h>
-
-#include <sstream>
+#include <llvm/Config/llvm-config.h>   // for LLVM_VERSION_MAJOR, LLVM_VERSI...
+#include <llvm/Support/raw_ostream.h>  // for errs, raw_ostream, raw_fd_ostream
 
 using std::string;
 
diff --git a/FactGenerator/src/main.cpp b/FactGenerator/src/main.cpp
index 9a206d5..0767073 100644
--- a/FactGenerator/src/main.cpp
+++ b/FactGenerator/src/main.cpp
@@ -1,19 +1,29 @@
-#include <llvm/Config/llvm-config.h>
-#include <llvm/IR/LLVMContext.h>
-#include <llvm/IR/Module.h>
-#include <llvm/IRReader/IRReader.h>
-#include <llvm/Support/SourceMgr.h>
-
-#include <boost/filesystem.hpp>
-#include <iostream>
-#include <string>
-
-#include "ContextSensitivity.hpp"
-#include "FactGenerator.hpp"
-#include "FactWriter.hpp"
-#include "Options.hpp"
-#include "ParseException.hpp"
-#include "factgen.hpp"
+#include <llvm/ADT/Optional.h>        // for Optional
+#include <llvm/Config/llvm-config.h>  // for LLVM_VERSION_MAJOR, LLVM...
+#include <llvm/IR/LLVMContext.h>      // for LLVMContext
+#include <llvm/IR/Module.h>           // for Module
+#include <llvm/IRReader/IRReader.h>   // for parseIRFile
+#include <llvm/Support/SourceMgr.h>   // for SMDiagnostic
+#include <stdlib.h>                   // for EXIT_FAILURE, EXIT_SUCCESS
+
+#include <boost/filesystem/operations.hpp>   // for canonical
+#include <boost/filesystem/path.hpp>         // for path
+#include <boost/filesystem/path_traits.hpp>  // for filesystem
+#include <iostream>                          // for operator<<, endl, basic_...
+#include <memory>                            // for unique_ptr
+#include <string>                            // for string
+#include <utility>                           // for move
+#include <vector>                            // for vector
+
+#include "ContextSensitivity.hpp"  // for ContextSensitivity, INSE...
+#include "FactGenerator.hpp"       // for FactGenerator
+#include "FactWriter.hpp"          // for FactWriter
+#include "Options.hpp"             // for Options
+#include "ParseException.hpp"      // for ParseException
+#include "factgen.hpp"             // for factgen
+namespace llvm {
+class DataLayout;
+}
 
 // Type aliases
 namespace fs = boost::filesystem;
diff --git a/FactGenerator/src/types.cpp b/FactGenerator/src/types.cpp
index af29452..c9d76b7 100644
--- a/FactGenerator/src/types.cpp
+++ b/FactGenerator/src/types.cpp
@@ -1,12 +1,16 @@
-#include <llvm/IR/DataLayout.h>
-#include <llvm/IR/Type.h>
-
-#include <string>
-
-#include "FactGenerator.hpp"
-#include "TypeAccumulator.hpp"
-#include "TypeVisitor.hpp"
-#include "predicate_groups.hpp"
+// IWYU pragma: no_include <boost/unordered/detail/implementation.hpp>
+#include <boost/unordered/unordered_set.hpp>  // for unordered_set<>...
+#include <string>                             // for allocator
+
+#include "FactGenerator.hpp"     // for FactGenerator
+#include "TypeAccumulator.hpp"   // for TypeAccumulator
+#include "TypeVisitor.hpp"       // for TypeVisitor
+#include "predicate_groups.hpp"  // for primitive_type
+
+// Forward decls
+namespace llvm {
+class DataLayout;
+}
 
 using cclyzer::FactGenerator;
 namespace pred = cclyzer::predicates;
diff --git a/FactGenerator/src/variables.cpp b/FactGenerator/src/variables.cpp
index 9ce2435..728f066 100644
--- a/FactGenerator/src/variables.cpp
+++ b/FactGenerator/src/variables.cpp
@@ -1,9 +1,16 @@
-#include <llvm/IR/Type.h>
+// IWYU pragma: no_include <boost/unordered/detail/implementation.hpp>
 
-#include <string>
+#include <llvm/ADT/StringRef.h>  // for StringRef, Stri...
+#include <llvm/IR/Function.h>    // for Function
+#include <stddef.h>              // for size_t
 
-#include "FactGenerator.hpp"
-#include "predicate_groups.hpp"
+#include <boost/unordered/unordered_map.hpp>  // for unordered_map<>...
+#include <string>                             // for string, operator+
+#include <type_traits>                        // for add_const<>::type
+#include <utility>                            // for tuple_element<>...
+
+#include "FactGenerator.hpp"     // for FactGenerator
+#include "predicate_groups.hpp"  // for variable, predi...
 
 using cclyzer::FactGenerator;
 namespace pred = cclyzer::predicates;
diff --git a/docker/dev.dockerfile b/docker/dev.dockerfile
index b98b8ad..54145fa 100644
--- a/docker/dev.dockerfile
+++ b/docker/dev.dockerfile
@@ -17,6 +17,7 @@ SHELL ["/bin/bash", "-c", "-o", "pipefail"]
 ENV DEBIAN_FRONTEND=noninteractive
 
 # cmake: Build system
+# iwyu: Linter
 # git: Later steps of Dockerfile
 # gnupg: Later steps of Dockerfile
 # ninja-build: Build system
@@ -31,6 +32,7 @@ ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update && \
     apt-get --yes install --no-install-recommends \
       cmake \
+      iwyu \
       git \
       gnupg \
       ninja-build \