diff --git a/tools/bugpoint/BugDriver.h b/tools/bugpoint/BugDriver.h
index 19fc80b8741..819379d6e9c 100644
--- a/tools/bugpoint/BugDriver.h
+++ b/tools/bugpoint/BugDriver.h
@@ -213,7 +213,7 @@ public:
   /// "bugpoint-ID.bc".
   ///
   void EmitProgressBitcode(const Module *M, const std::string &ID,
-                           bool NoFlyer = false);
+                           bool NoFlyer = false) const;
 
   /// deleteInstructionFromProgram - This method clones the current Program and
   /// deletes the specified instruction from the cloned module.  It then runs a
@@ -261,7 +261,8 @@ public:
   /// or failed, unless Quiet is set.  ExtraArgs specifies additional arguments
   /// to pass to the child bugpoint instance.
   ///
-  bool runPasses(const std::vector<const PassInfo*> &PassesToRun,
+  bool runPasses(Module *Program,
+                 const std::vector<const PassInfo*> &PassesToRun,
                  std::string &OutputFilename, bool DeleteOutput = false,
                  bool Quiet = false, unsigned NumExtraArgs = 0,
                  const char * const *ExtraArgs = NULL) const;
@@ -289,7 +290,7 @@ private:
   bool runPasses(const std::vector<const PassInfo*> &PassesToRun,
                  bool DeleteOutput = true) const {
     std::string Filename;
-    return runPasses(PassesToRun, Filename, DeleteOutput);
+    return runPasses(Program, PassesToRun, Filename, DeleteOutput);
   }
 
   /// runAsChild - The actual "runPasses" guts that runs in a child process.
diff --git a/tools/bugpoint/CrashDebugger.cpp b/tools/bugpoint/CrashDebugger.cpp
index 272ec7eb75d..735adc57384 100644
--- a/tools/bugpoint/CrashDebugger.cpp
+++ b/tools/bugpoint/CrashDebugger.cpp
@@ -68,7 +68,7 @@ ReducePassList::doTest(std::vector<const PassInfo*> &Prefix,
     outs() << "Checking to see if these passes crash: "
            << getPassesString(Prefix) << ": ";
     std::string PfxOutput;
-    if (BD.runPasses(Prefix, PfxOutput))
+    if (BD.runPasses(BD.getProgram(), Prefix, PfxOutput))
       return KeepPrefix;
 
     PrefixOutput.set(PfxOutput);
diff --git a/tools/bugpoint/FindBugs.cpp b/tools/bugpoint/FindBugs.cpp
index 4fd597ee119..d4597dc1041 100644
--- a/tools/bugpoint/FindBugs.cpp
+++ b/tools/bugpoint/FindBugs.cpp
@@ -62,7 +62,7 @@ bool BugDriver::runManyPasses(const std::vector<const PassInfo*> &AllPasses,
     }
     
     std::string Filename;
-    if(runPasses(PassesToRun, Filename, false)) {
+    if(runPasses(Program, PassesToRun, Filename, false)) {
       outs() << "\n";
       outs() << "Optimizer passes caused failure!\n\n";
       debugOptimizerCrash();
diff --git a/tools/bugpoint/Miscompilation.cpp b/tools/bugpoint/Miscompilation.cpp
index db4940f4bf7..0ae883c4841 100644
--- a/tools/bugpoint/Miscompilation.cpp
+++ b/tools/bugpoint/Miscompilation.cpp
@@ -67,7 +67,8 @@ ReduceMiscompilingPasses::doTest(std::vector<const PassInfo*> &Prefix,
          << "' compiles correctly: ";
 
   std::string BitcodeResult;
-  if (BD.runPasses(Suffix, BitcodeResult, false/*delete*/, true/*quiet*/)) {
+  if (BD.runPasses(BD.getProgram(), Suffix, BitcodeResult, false/*delete*/,
+                   true/*quiet*/)) {
     errs() << " Error running this sequence of passes"
            << " on the input program!\n";
     BD.setPassesToRun(Suffix);
@@ -104,7 +105,8 @@ ReduceMiscompilingPasses::doTest(std::vector<const PassInfo*> &Prefix,
   // kept passes, we can update our bitcode file to include the result of the
   // prefix passes, then discard the prefix passes.
   //
-  if (BD.runPasses(Prefix, BitcodeResult, false/*delete*/, true/*quiet*/)) {
+  if (BD.runPasses(BD.getProgram(), Prefix, BitcodeResult, false/*delete*/,
+                   true/*quiet*/)) {
     errs() << " Error running this sequence of passes"
            << " on the input program!\n";
     BD.setPassesToRun(Prefix);
@@ -144,7 +146,8 @@ ReduceMiscompilingPasses::doTest(std::vector<const PassInfo*> &Prefix,
             << getPassesString(Prefix) << "' passes: ";
 
   OwningPtr<Module> OriginalInput(BD.swapProgramIn(PrefixOutput.take()));
-  if (BD.runPasses(Suffix, BitcodeResult, false/*delete*/, true/*quiet*/)) {
+  if (BD.runPasses(BD.getProgram(), Suffix, BitcodeResult, false/*delete*/,
+                   true/*quiet*/)) {
     errs() << " Error running this sequence of passes"
            << " on the input program!\n";
     BD.setPassesToRun(Suffix);
diff --git a/tools/bugpoint/OptimizerDriver.cpp b/tools/bugpoint/OptimizerDriver.cpp
index 48936caf5fd..a6b90dc44b2 100644
--- a/tools/bugpoint/OptimizerDriver.cpp
+++ b/tools/bugpoint/OptimizerDriver.cpp
@@ -66,7 +66,8 @@ bool BugDriver::writeProgramToFile(const std::string &Filename,
 /// to a file named "bugpoint-ID.bc".
 ///
 void BugDriver::EmitProgressBitcode(const Module *M,
-                                    const std::string &ID, bool NoFlyer) {
+                                    const std::string &ID,
+                                    bool NoFlyer)  const {
   // Output the input to the current pass to a bitcode file, emit a message
   // telling the user how to reproduce it: opt -foo blah.bc
   //
@@ -125,7 +126,8 @@ cl::opt<bool> SilencePasses("silence-passes", cl::desc("Suppress output of runni
 /// outs() a single line message indicating whether compilation was successful
 /// or failed.
 ///
-bool BugDriver::runPasses(const std::vector<const PassInfo*> &Passes,
+bool BugDriver::runPasses(Module *Program,
+                          const std::vector<const PassInfo*> &Passes,
                           std::string &OutputFilename, bool DeleteOutput,
                           bool Quiet, unsigned NumExtraArgs,
                           const char * const *ExtraArgs) const {
@@ -239,24 +241,19 @@ Module *BugDriver::runPassesOn(Module *M,
                                const std::vector<const PassInfo*> &Passes,
                                bool AutoDebugCrashes, unsigned NumExtraArgs,
                                const char * const *ExtraArgs) {
-  Module *OldProgram = swapProgramIn(M);
   std::string BitcodeResult;
-  if (runPasses(Passes, BitcodeResult, false/*delete*/, true/*quiet*/,
+  if (runPasses(M, Passes, BitcodeResult, false/*delete*/, true/*quiet*/,
                 NumExtraArgs, ExtraArgs)) {
     if (AutoDebugCrashes) {
       errs() << " Error running this sequence of passes"
              << " on the input program!\n";
-      delete OldProgram;
-      EmitProgressBitcode(Program, "pass-error",  false);
+      delete swapProgramIn(M);
+      EmitProgressBitcode(M, "pass-error",  false);
       exit(debugOptimizerCrash());
     }
-    swapProgramIn(OldProgram);
     return 0;
   }
 
-  // Restore the current program.
-  swapProgramIn(OldProgram);
-
   Module *Ret = ParseInputFile(BitcodeResult, Context);
   if (Ret == 0) {
     errs() << getToolName() << ": Error reading bitcode file '"