Index: llvm/trunk/test/tools/llvm-objcopy/segment-shift.test
===================================================================
--- llvm/trunk/test/tools/llvm-objcopy/segment-shift.test
+++ llvm/trunk/test/tools/llvm-objcopy/segment-shift.test
@@ -0,0 +1,70 @@
+# RUN: yaml2obj %s -o %t
+# RUN: llvm-objcopy %t %t2
+# RUN: llvm-readobj -program-headers %t2 | FileCheck %s
+
+!ELF
+FileHeader:
+  Class:           ELFCLASS64
+  Data:            ELFDATA2LSB
+  Type:            ET_EXEC
+  Machine:         EM_X86_64
+Sections:
+  - Name:            .text
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    Address:         0x1000
+    AddressAlign:    0x1000
+    Size:            0x1000
+  - Name:            .text2
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    Address:         0x2000
+    AddressAlign:    0x1000
+    Size:            0x1000
+  - Name:            .text3
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    Address:         0x3000
+    AddressAlign:    0x1000
+    Size:            0x1000
+ProgramHeaders:
+  - Type: PT_LOAD
+    Flags: [ PF_R ]
+    VAddr: 0x1000
+    PAddr: 0x1000
+    Sections:
+      - Section: .text
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    VAddr: 0x3000
+    PAddr: 0x3000
+    Sections:
+      - Section: .text3
+
+# CHECK:     ProgramHeaders [
+# CHECK-NEXT:  ProgramHeader {
+# CHECK-NEXT:    Type: PT_LOAD (0x1)
+# CHECK-NEXT:    Offset: 0x1000
+# CHECK-NEXT:    VirtualAddress: 0x1000
+# CHECK-NEXT:    PhysicalAddress: 0x1000
+# CHECK-NEXT:    FileSize: 4096
+# CHECK-NEXT:    MemSize: 4096
+# CHECK-NEXT:    Flags [ (0x4)
+# CHECK-NEXT:      PF_R (0x4)
+# CHECK-NEXT:    ]
+# CHECK-NEXT:    Alignment: 4096
+# CHECK-NEXT:  }
+# CHECK-NEXT:  ProgramHeader {
+# CHECK-NEXT:    Type: PT_LOAD (0x1)
+# CHECK-NEXT:    Offset: 0x2000
+# CHECK-NEXT:    VirtualAddress: 0x3000
+# CHECK-NEXT:    PhysicalAddress: 0x3000
+# CHECK-NEXT:    FileSize: 4096
+# CHECK-NEXT:    MemSize: 4096
+# CHECK-NEXT:    Flags [ (0x5)
+# CHECK-NEXT:      PF_R (0x4)
+# CHECK-NEXT:      PF_X (0x1)
+# CHECK-NEXT:    ]
+# CHECK-NEXT:    Alignment: 4096
+# CHECK-NEXT:  }
+# CHECK-NEXT:]
Index: llvm/trunk/tools/llvm-objcopy/Object.h
===================================================================
--- llvm/trunk/tools/llvm-objcopy/Object.h
+++ llvm/trunk/tools/llvm-objcopy/Object.h
@@ -93,7 +93,6 @@
   Segment *ParentSegment = nullptr;
 
   Segment(llvm::ArrayRef<uint8_t> Data) : Contents(Data) {}
-  void finalize();
   const SectionBase *firstSection() const {
     if (!Sections.empty())
       return *Sections.begin();
Index: llvm/trunk/tools/llvm-objcopy/Object.cpp
===================================================================
--- llvm/trunk/tools/llvm-objcopy/Object.cpp
+++ llvm/trunk/tools/llvm-objcopy/Object.cpp
@@ -30,18 +30,6 @@
   Phdr.p_align = Align;
 }
 
-void Segment::finalize() {
-  auto FirstSec = firstSection();
-  if (FirstSec) {
-    // It is possible for a gap to be at the begining of a segment. Because of
-    // this we need to compute the new offset based on how large this gap was
-    // in the source file. Section layout should have already ensured that this
-    // space is not used for something else.
-    uint64_t OriginalOffset = Offset;
-    Offset = FirstSec->Offset - (FirstSec->OriginalOffset - OriginalOffset);
-  }
-}
-
 void Segment::writeSegment(FileOutputBuffer &Out) const {
   uint8_t *Buf = Out.getBufferStart() + Offset;
   // We want to maintain segments' interstitial data and contents exactly.
@@ -656,8 +644,8 @@
     } else {
       Offset = alignTo(Offset, Segment->Align == 0 ? 1 : Segment->Align);
       Segment->Offset = Offset;
-      Offset += Segment->FileSize;
     }
+    Offset = std::max(Offset, Segment->Offset + Segment->FileSize);
   }
   // Now the offset of every segment has been set we can assign the offsets
   // of each section. For sections that are covered by a segment we should use
@@ -673,7 +661,7 @@
       Section->Offset =
           Segment->Offset + (Section->OriginalOffset - Segment->OriginalOffset);
     } else {
-      Offset = alignTo(Offset, Section->Offset);
+      Offset = alignTo(Offset, Section->Align == 0 ? 1 : Section->Align);
       Section->Offset = Offset;
       if (Section->Type != SHT_NOBITS)
         Offset += Section->Size;
@@ -720,9 +708,6 @@
     Section->NameIndex = this->SectionNames->findIndex(Section->Name);
     Section->finalize();
   }
-
-  for (auto &Segment : this->Segments)
-    Segment->finalize();
 }
 
 template <class ELFT> size_t BinaryObject<ELFT>::totalSize() const {
@@ -742,8 +727,6 @@
 }
 
 template <class ELFT> void BinaryObject<ELFT>::finalize() {
-  for (auto &Segment : this->Segments)
-    Segment->finalize();
 
   // Put all segments in offset order.
   auto CompareSegments = [](const SegPtr &A, const SegPtr &B) {