This is how MallocChecker looks with options used.

http://reviews.llvm.org/D3967

Files:
  include/clang/StaticAnalyzer/Core/AnalyzerOptions.h
  lib/StaticAnalyzer/Checkers/Checkers.td
  lib/StaticAnalyzer/Checkers/MallocChecker.cpp
  lib/StaticAnalyzer/Core/AnalyzerOptions.cpp
  test/Analysis/free.c
  test/Analysis/malloc-annotations.c
  test/Analysis/outofbound.c
  test/Analysis/undef-buffers.c
Index: include/clang/StaticAnalyzer/Core/AnalyzerOptions.h
===================================================================
--- include/clang/StaticAnalyzer/Core/AnalyzerOptions.h
+++ include/clang/StaticAnalyzer/Core/AnalyzerOptions.h
@@ -27,6 +27,9 @@
 class DiagnosticsEngine;
 class Preprocessor;
 class LangOptions;
+namespace ento {
+class CheckerBase;
+}
 
 /// Analysis - Set of available source code analyses.
 enum Analyses {
@@ -132,7 +135,7 @@
   AnalysisPurgeMode AnalysisPurgeOpt;
   
   std::string AnalyzeSpecificFunction;
-  
+
   /// \brief The maximum number of times the analyzer visits a block.
   unsigned maxBlockVisitOnPath;
   
@@ -245,18 +248,62 @@
   /// \sa getMaxNodesPerTopLevelFunction
   Optional<unsigned> MaxNodesPerTopLevelFunction;
 
+  /// A helper function that retrieves option for a given full-qualified
+  /// checker name.
+  /// Options for checkers can be specified via 'analyzer-config' command-line
+  /// option.
+  /// Example:
+  /// @code-analyzer-config unix.Malloc:OptionName=CheckerOptionValue @endcode
+  /// or @code-analyzer-config unix:OptionName=GroupOptionValue @endcode
+  /// for groups of checkers
+  /// @param [in] CheckerName  Full-qualified checker name, like
+  /// alpha.unix.StreamChecker
+  /// @param [in] OptionName  Name of the option to get
+  /// @param [in] Default  Default value if no option is specified
+  /// @retval CheckerOptionValue  An option for a checker if it was specified
+  /// @retval GroupOptionValue  An option for group if it was specified and no
+  /// checker-specific options were found. The closer group to checker,
+  /// the more priority it has. For example, @c coregroup.subgroup has more
+  /// priority than @c coregroup for @c coregroup.subgroup.CheckerName checker
+  /// @retval Default  If nor checker option, nor group option was found
+  StringRef getCheckerOption(StringRef CheckerName, StringRef OptionName,
+                             StringRef Default) const;
+
 public:
   /// Interprets an option's string value as a boolean.
   ///
   /// Accepts the strings "true" and "false".
   /// If an option value is not provided, returns the given \p DefaultVal.
-  bool getBooleanOption(StringRef Name, bool DefaultVal);
+  /// @param [in] Name Name for option to retrieve
+  /// @param [in] DefaultVal Default value returned if no such option was
+  /// specified
+  /// @param [in] C Optional parameter that may be used to retrieve
+  /// checker-related option for a given checker
+  bool getBooleanOption(StringRef Name, bool DefaultVal,
+                        const ento::CheckerBase *C = nullptr);
 
   /// Variant that accepts a Optional value to cache the result.
-  bool getBooleanOption(Optional<bool> &V, StringRef Name, bool DefaultVal);
+  ///
+  /// @param [in,out] V Return value storage, returned if parameter contains
+  /// an existing valid option, else it is used to store a return value
+  /// @param [in] Name Name for option to retrieve
+  /// @param [in] DefaultVal Default value returned if no such option was
+  /// specified
+  /// @param [in] C Optional parameter that may be used to retrieve
+  /// checker-related option for a given checker
+  bool getBooleanOption(Optional<bool> &V, StringRef Name, bool DefaultVal,
+                        const ento::CheckerBase *C = nullptr);
 
   /// Interprets an option's string value as an integer value.
-  int getOptionAsInteger(StringRef Name, int DefaultVal);
+  ///
+  /// If an option value is not provided, returns the given \p DefaultVal.
+  /// @param [in] Name Name for option to retrieve
+  /// @param [in] DefaultVal Default value returned if no such option was
+  /// specified
+  /// @param [in] C Optional parameter that may be used to retrieve
+  /// checker-related option for a given checker
+  int getOptionAsInteger(StringRef Name, int DefaultVal,
+                         const ento::CheckerBase *C = nullptr);
 
   /// \brief Retrieves and sets the UserMode. This is a high-level option,
   /// which is used to set other low-level options. It is not accessible
Index: lib/StaticAnalyzer/Checkers/Checkers.td
===================================================================
--- lib/StaticAnalyzer/Checkers/Checkers.td
+++ lib/StaticAnalyzer/Checkers/Checkers.td
@@ -295,7 +299,7 @@
   HelpText<"Check calls to various UNIX/Posix functions">,
   DescFile<"UnixAPIChecker.cpp">;
 
-def MallocPessimistic : Checker<"Malloc">,
+def MallocChecker: Checker<"Malloc">,
   HelpText<"Check for memory leaks, double free, and use-after-free problems. Traces memory managed by malloc()/free().">,
   DescFile<"MallocChecker.cpp">;
   
@@ -315,10 +319,6 @@
   HelpText<"Check improper use of chroot">,
   DescFile<"ChrootChecker.cpp">;
 
-def MallocOptimistic : Checker<"MallocWithAnnotations">,
-  HelpText<"Check for memory leaks, double free, and use-after-free problems. Traces memory managed by malloc()/free(). Assumes that all user-defined functions which might free a pointer are annotated.">,
-  DescFile<"MallocChecker.cpp">;
-
 def PthreadLockChecker : Checker<"PthreadLock">,
   HelpText<"Simple lock -> unlock checker">,
   DescFile<"PthreadLockChecker.cpp">;
Index: lib/StaticAnalyzer/Checkers/MallocChecker.cpp
===================================================================
--- lib/StaticAnalyzer/Checkers/MallocChecker.cpp
+++ lib/StaticAnalyzer/Checkers/MallocChecker.cpp
@@ -165,14 +165,15 @@
   /// In pessimistic mode, the checker assumes that it does not know which
   /// functions might free the memory.
   enum CheckKind {
-    CK_MallocPessimistic,
-    CK_MallocOptimistic,
+    CK_MallocChecker,
     CK_NewDeleteChecker,
     CK_NewDeleteLeaksChecker,
     CK_MismatchedDeallocatorChecker,
     CK_NumCheckKinds
   };
 
+  DefaultBool IsOptimistic;
+
   DefaultBool ChecksEnabled[CK_NumCheckKinds];
   CheckName CheckNames[CK_NumCheckKinds];
 
@@ -524,7 +525,7 @@
       return true;
   }
 
-  if (ChecksEnabled[CK_MallocOptimistic] && FD->hasAttrs())
+  if (IsOptimistic && FD->hasAttrs())
     for (const auto *I : FD->specific_attrs<OwnershipAttr>())
       if (I->getOwnKind() == OwnershipAttr::Returns)
         return true;
@@ -543,7 +544,7 @@
       return true;
   }
 
-  if (ChecksEnabled[CK_MallocOptimistic] && FD->hasAttrs())
+  if (IsOptimistic && FD->hasAttrs())
     for (const auto *I : FD->specific_attrs<OwnershipAttr>())
       if (I->getOwnKind() == OwnershipAttr::Takes ||
           I->getOwnKind() == OwnershipAttr::Holds)
@@ -733,8 +734,7 @@
     }
   }
 
-  if (ChecksEnabled[CK_MallocOptimistic] ||
-      ChecksEnabled[CK_MismatchedDeallocatorChecker]) {
+  if (IsOptimistic || ChecksEnabled[CK_MismatchedDeallocatorChecker]) {
     // Check all the attributes, if there are any.
     // There can be multiple of these attributes.
     if (FD->hasAttrs())
@@ -1202,11 +1202,8 @@
 MallocChecker::getCheckIfTracked(AllocationFamily Family) const {
   switch (Family) {
   case AF_Malloc: {
-    if (ChecksEnabled[CK_MallocOptimistic]) {
-      return CK_MallocOptimistic;
-    } else if (ChecksEnabled[CK_MallocPessimistic]) {
-      return CK_MallocPessimistic;
-    }
+    if (ChecksEnabled[CK_MallocChecker])
+      return CK_MallocChecker;
     return Optional<MallocChecker::CheckKind>();
   }
   case AF_CXXNew:
@@ -1328,9 +1325,7 @@
                                   SourceRange Range, 
                                   const Expr *DeallocExpr) const {
 
-  if (!ChecksEnabled[CK_MallocOptimistic] &&
-      !ChecksEnabled[CK_MallocPessimistic] &&
-      !ChecksEnabled[CK_NewDeleteChecker])
+  if (!ChecksEnabled[CK_MallocChecker] && !ChecksEnabled[CK_NewDeleteChecker])
     return;
 
   Optional<MallocChecker::CheckKind> CheckKind =
@@ -1434,9 +1429,7 @@
                                      SourceRange Range, const Expr *DeallocExpr,
                                      const Expr *AllocExpr) const {
 
-  if (!ChecksEnabled[CK_MallocOptimistic] &&
-      !ChecksEnabled[CK_MallocPessimistic] &&
-      !ChecksEnabled[CK_NewDeleteChecker])
+  if (!ChecksEnabled[CK_MallocChecker] && !ChecksEnabled[CK_NewDeleteChecker])
     return;
 
   Optional<MallocChecker::CheckKind> CheckKind =
@@ -1490,9 +1483,7 @@
 void MallocChecker::ReportUseAfterFree(CheckerContext &C, SourceRange Range,
                                        SymbolRef Sym) const {
 
-  if (!ChecksEnabled[CK_MallocOptimistic] &&
-      !ChecksEnabled[CK_MallocPessimistic] &&
-      !ChecksEnabled[CK_NewDeleteChecker])
+  if (!ChecksEnabled[CK_MallocChecker] && !ChecksEnabled[CK_NewDeleteChecker])
     return;
 
   Optional<MallocChecker::CheckKind> CheckKind = getCheckIfTracked(C, Sym);
@@ -1518,9 +1509,7 @@
                                      bool Released, SymbolRef Sym, 
                                      SymbolRef PrevSym) const {
 
-  if (!ChecksEnabled[CK_MallocOptimistic] &&
-      !ChecksEnabled[CK_MallocPessimistic] &&
-      !ChecksEnabled[CK_NewDeleteChecker])
+  if (!ChecksEnabled[CK_MallocChecker] && !ChecksEnabled[CK_NewDeleteChecker])
     return;
 
   Optional<MallocChecker::CheckKind> CheckKind = getCheckIfTracked(C, Sym);
@@ -1731,8 +1720,7 @@
 void MallocChecker::reportLeak(SymbolRef Sym, ExplodedNode *N,
                                CheckerContext &C) const {
 
-  if (!ChecksEnabled[CK_MallocOptimistic] &&
-      !ChecksEnabled[CK_MallocPessimistic] &&
+  if (!ChecksEnabled[CK_MallocChecker] &&
       !ChecksEnabled[CK_NewDeleteLeaksChecker])
     return;
 
@@ -1865,8 +1853,7 @@
     if (!FD)
       return;
 
-    if ((ChecksEnabled[CK_MallocOptimistic] ||
-         ChecksEnabled[CK_MallocPessimistic]) &&
+    if (ChecksEnabled[CK_MallocChecker] &&
         isFreeFunction(FD, C.getASTContext()))
       return;
 
@@ -2371,6 +2358,8 @@
 void ento::registerNewDeleteLeaksChecker(CheckerManager &mgr) {
   registerCStringCheckerBasic(mgr);
   MallocChecker *checker = mgr.registerChecker<MallocChecker>();
+  checker->IsOptimistic = mgr.getAnalyzerOptions().getBooleanOption(
+        "Optimistic", false, checker);
   checker->ChecksEnabled[MallocChecker::CK_NewDeleteLeaksChecker] = true;
   checker->CheckNames[MallocChecker::CK_NewDeleteLeaksChecker] =
       mgr.getCurrentCheckName();
@@ -2384,11 +2373,12 @@
   void ento::register##name(CheckerManager &mgr) {                             \
     registerCStringCheckerBasic(mgr);                                          \
     MallocChecker *checker = mgr.registerChecker<MallocChecker>();             \
+    checker->IsOptimistic = mgr.getAnalyzerOptions().getBooleanOption(         \
+          "Optimistic", false, checker);                                       \
     checker->ChecksEnabled[MallocChecker::CK_##name] = true;                   \
     checker->CheckNames[MallocChecker::CK_##name] = mgr.getCurrentCheckName(); \
   }
 
-REGISTER_CHECKER(MallocPessimistic)
-REGISTER_CHECKER(MallocOptimistic)
+REGISTER_CHECKER(MallocChecker)
 REGISTER_CHECKER(NewDeleteChecker)
 REGISTER_CHECKER(MismatchedDeallocatorChecker)
Index: lib/StaticAnalyzer/Core/AnalyzerOptions.cpp
===================================================================
--- lib/StaticAnalyzer/Core/AnalyzerOptions.cpp
+++ lib/StaticAnalyzer/Core/AnalyzerOptions.cpp
@@ -13,12 +13,14 @@
 //===----------------------------------------------------------------------===//
 
 #include "clang/StaticAnalyzer/Core/AnalyzerOptions.h"
+#include "clang/StaticAnalyzer/Core/Checker.h"
 #include "llvm/ADT/SmallString.h"
 #include "llvm/ADT/StringSwitch.h"
 #include "llvm/Support/ErrorHandling.h"
 #include "llvm/Support/raw_ostream.h"
 
 using namespace clang;
+using namespace ento;
 using namespace llvm;
 
 AnalyzerOptions::UserModeKind AnalyzerOptions::getUserMode() {
@@ -98,11 +100,33 @@
 
 static StringRef toString(bool b) { return b ? "true" : "false"; }
 
-bool AnalyzerOptions::getBooleanOption(StringRef Name, bool DefaultVal) {
+StringRef AnalyzerOptions::getCheckerOption(StringRef CheckerName,
+                                            StringRef OptionName,
+                                            StringRef Default) const {
+  std::string Name = CheckerName;
+  std::string Suffix = ":" + OptionName.str();
+  // Search for a category option if option for checker is not specified
+  ConfigTable::const_iterator e = Config.end();
+  while (!Name.empty()) {
+    ConfigTable::const_iterator i = Config.find(Name + Suffix);
+    if (i != e)
+      return StringRef(i->getValue());
+    size_t pos = Name.rfind('.');
+    if (pos == std::string::npos)
+      return Default;
+    Name = Name.substr(0, pos);
+  }
+  return Default;
+}
+
+bool AnalyzerOptions::getBooleanOption(StringRef Name, bool DefaultVal,
+                                       const CheckerBase *C) {
   // FIXME: We should emit a warning here if the value is something other than
   // "true", "false", or the empty string (meaning the default value),
   // but the AnalyzerOptions doesn't have access to a diagnostic engine.
-  StringRef V(Config.GetOrCreateValue(Name, toString(DefaultVal)).getValue());
+  StringRef Default = toString(DefaultVal);
+  StringRef V = C ? getCheckerOption(C->getTagDescription(), Name, Default)
+                  : StringRef(Config.GetOrCreateValue(Name,Default).getValue());
   return llvm::StringSwitch<bool>(V)
       .Case("true", true)
       .Case("false", false)
@@ -110,9 +134,9 @@
 }
 
 bool AnalyzerOptions::getBooleanOption(Optional<bool> &V, StringRef Name,
-                                       bool DefaultVal) {
+                                       bool DefaultVal, const CheckerBase *C) {
   if (!V.hasValue())
-    V = getBooleanOption(Name, DefaultVal);
+    V = getBooleanOption(Name, DefaultVal, C);
   return V.getValue();
 }
 
@@ -196,12 +220,14 @@
                           /* Default = */ false);
 }
 
-int AnalyzerOptions::getOptionAsInteger(StringRef Name, int DefaultVal) {
+int AnalyzerOptions::getOptionAsInteger(StringRef Name, int DefaultVal,
+                                        const CheckerBase *C) {
   SmallString<10> StrBuf;
   llvm::raw_svector_ostream OS(StrBuf);
   OS << DefaultVal;
   
-  StringRef V(Config.GetOrCreateValue(Name, OS.str()).getValue());
+  StringRef V = C ? getCheckerOption(C->getTagDescription(), Name, OS.str())
+                  : StringRef(Config.GetOrCreateValue(Name,OS.str()).getValue());
   int Res = DefaultVal;
   bool b = V.getAsInteger(10, Res);
   assert(!b && "analyzer-config option should be numeric");
Index: test/Analysis/free.c
===================================================================
--- test/Analysis/free.c
+++ test/Analysis/free.c
@@ -1,5 +1,5 @@
 // RUN: %clang_cc1 -analyze -analyzer-store=region -analyzer-checker=core,unix.Malloc -fblocks -verify %s
-// RUN: %clang_cc1 -analyze -analyzer-store=region -analyzer-checker=core,alpha.unix.MallocWithAnnotations -fblocks -verify %s
+// RUN: %clang_cc1 -analyze -analyzer-store=region -analyzer-checker=core,unix.Malloc -fblocks -verify -analyzer-config unix.Malloc:Optimistic=true %s
 void free(void *);
 
 void t1 () {
Index: test/Analysis/malloc-annotations.c
===================================================================
--- test/Analysis/malloc-annotations.c
+++ test/Analysis/malloc-annotations.c
@@ -1,4 +1,5 @@
-// RUN: %clang_cc1 -analyze -analyzer-checker=core,alpha.deadcode.UnreachableCode,alpha.core.CastSize,alpha.unix.MallocWithAnnotations -analyzer-store=region -verify %s
+// RUN: %clang_cc1 -analyze -analyzer-checker=core,alpha.deadcode.UnreachableCode,alpha.core.CastSize,unix.Malloc -analyzer-store=region -verify -analyzer-config unix:Optimistic=true %s
+// RUN: %clang_cc1 -analyze -analyzer-checker=core,alpha.deadcode.UnreachableCode,alpha.core.CastSize,unix.Malloc -analyzer-store=region -verify -analyzer-config unix.Malloc:Optimistic=true %s
 typedef __typeof(sizeof(int)) size_t;
 void *malloc(size_t);
 void free(void *);
Index: test/Analysis/outofbound.c
===================================================================
--- test/Analysis/outofbound.c
+++ test/Analysis/outofbound.c
@@ -1,4 +1,4 @@
-// RUN: %clang_cc1 -Wno-array-bounds -analyze -analyzer-checker=core,alpha.unix,alpha.security.ArrayBound -analyzer-store=region -verify %s
+// RUN: %clang_cc1 -Wno-array-bounds -analyze -analyzer-checker=core,unix,alpha.security.ArrayBound -analyzer-store=region -verify -analyzer-config unix:Optimistic=true %s
 
 typedef __typeof(sizeof(int)) size_t;
 void *malloc(size_t);
Index: test/Analysis/undef-buffers.c
===================================================================
--- test/Analysis/undef-buffers.c
+++ test/Analysis/undef-buffers.c
@@ -1,4 +1,4 @@
-// RUN: %clang_cc1 -analyze -analyzer-checker=core,alpha.unix,core.uninitialized -analyzer-store=region -verify %s
+// RUN: %clang_cc1 -analyze -analyzer-checker=core,unix,core.uninitialized -analyzer-store=region -verify -analyzer-config unix:Optimistic=true %s
 typedef __typeof(sizeof(int)) size_t;
 void *malloc(size_t);
 void free(void *);
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