diff --git a/src/build.cc b/src/build.cc
index 76ff93af03..6903e45306 100644
--- a/src/build.cc
+++ b/src/build.cc
@@ -95,15 +95,20 @@ bool Plan::AddTarget(const Node* target, string* err) {
 bool Plan::AddSubTarget(const Node* node, const Node* dependent, string* err,
                         set<Edge*>* dyndep_walk) {
   Edge* edge = node->in_edge();
-  if (!edge) {  // Leaf node.
-    if (node->dirty()) {
-      string referenced;
-      if (dependent)
-        referenced = ", needed by '" + dependent->path() + "',";
-      *err = "'" + node->path() + "'" + referenced + " missing "
-             "and no known rule to make it";
-    }
-    return false;
+  if (!edge) {
+     // Leaf node, this can be either a regular input from the manifest
+     // (e.g. a source file), or an implicit input from a depfile or dyndep
+     // file. In the first case, a dirty flag means the file is missing,
+     // and the build should stop. In the second, do not do anything here
+     // since there is no producing edge to add to the plan.
+     if (node->dirty() && !node->generated_by_dep_loader()) {
+       string referenced;
+       if (dependent)
+         referenced = ", needed by '" + dependent->path() + "',";
+       *err = "'" + node->path() + "'" + referenced +
+              " missing and no known rule to make it";
+     }
+     return false;
   }
 
   if (edge->outputs_ready())
diff --git a/src/build_test.cc b/src/build_test.cc
index d32ad3e4c6..5ed8245e25 100644
--- a/src/build_test.cc
+++ b/src/build_test.cc
@@ -986,9 +986,19 @@ TEST_F(BuildTest, DepFileOK) {
   ASSERT_EQ(1u, fs_.files_read_.size());
   EXPECT_EQ("foo.o.d", fs_.files_read_[0]);
 
-  // Expect three new edges: one generating foo.o, and two more from
-  // loading the depfile.
-  ASSERT_EQ(orig_edges + 3, (int)state_.edges_.size());
+  // Expect one new edge generating foo.o. Loading the depfile should have
+  // added nodes, but not phony edges to the graph.
+  ASSERT_EQ(orig_edges + 1, (int)state_.edges_.size());
+
+  // Verify that nodes for blah.h and bar.h were added and that they
+  // are marked as generated by a dep loader.
+  ASSERT_FALSE(state_.LookupNode("foo.o")->generated_by_dep_loader());
+  ASSERT_FALSE(state_.LookupNode("foo.c")->generated_by_dep_loader());
+  ASSERT_TRUE(state_.LookupNode("blah.h"));
+  ASSERT_TRUE(state_.LookupNode("blah.h")->generated_by_dep_loader());
+  ASSERT_TRUE(state_.LookupNode("bar.h"));
+  ASSERT_TRUE(state_.LookupNode("bar.h")->generated_by_dep_loader());
+
   // Expect our edge to now have three inputs: foo.c and two headers.
   ASSERT_EQ(3u, edge->inputs_.size());
 
@@ -1154,7 +1164,6 @@ TEST_F(BuildTest, DepFileCanonicalize) {
   ASSERT_NO_FATAL_FAILURE(AssertParse(&state_,
 "rule cc\n  command = cc $in\n  depfile = $out.d\n"
 "build gen/stuff\\things/foo.o: cc x\\y/z\\foo.c\n"));
-  Edge* edge = state_.edges_.back();
 
   fs_.Create("x/y/z/foo.c", "");
   GetNode("bar.h")->MarkDirty();  // Mark bar.h as missing.
@@ -1167,10 +1176,10 @@ TEST_F(BuildTest, DepFileCanonicalize) {
   // The depfile path does not get Canonicalize as it seems unnecessary.
   EXPECT_EQ("gen/stuff\\things/foo.o.d", fs_.files_read_[0]);
 
-  // Expect three new edges: one generating foo.o, and two more from
-  // loading the depfile.
-  ASSERT_EQ(orig_edges + 3, (int)state_.edges_.size());
+  // Expect one new edge enerating foo.o.
+  ASSERT_EQ(orig_edges + 1, (int)state_.edges_.size());
   // Expect our edge to now have three inputs: foo.c and two headers.
+  Edge* edge = state_.edges_.back();
   ASSERT_EQ(3u, edge->inputs_.size());
 
   // Expect the command line we generate to only use the original input, and
@@ -2968,9 +2977,9 @@ TEST_F(BuildWithDepsLogTest, DepFileOKDepsLog) {
     EXPECT_TRUE(builder.AddTarget("fo o.o", &err));
     ASSERT_EQ("", err);
 
-    // Expect three new edges: one generating fo o.o, and two more from
-    // loading the depfile.
-    ASSERT_EQ(3u, state.edges_.size());
+    // Expect one new edge generating fo o.o, loading the depfile should
+    // note generate new edges.
+    ASSERT_EQ(1u, state.edges_.size());
     // Expect our edge to now have three inputs: foo.c and two headers.
     ASSERT_EQ(3u, edge->inputs_.size());
 
@@ -3110,16 +3119,14 @@ TEST_F(BuildWithDepsLogTest, DepFileDepsLogCanonicalize) {
     Builder builder(&state, config_, NULL, &deps_log, &fs_, &status_, 0);
     builder.command_runner_.reset(&command_runner_);
 
-    Edge* edge = state.edges_.back();
-
     state.GetNode("bar.h", 0)->MarkDirty();  // Mark bar.h as missing.
     EXPECT_TRUE(builder.AddTarget("a/b/c/d/e/fo o.o", &err));
     ASSERT_EQ("", err);
 
-    // Expect three new edges: one generating fo o.o, and two more from
-    // loading the depfile.
-    ASSERT_EQ(3u, state.edges_.size());
+    // Expect one new edge generating fo o.o.
+    ASSERT_EQ(1u, state.edges_.size());
     // Expect our edge to now have three inputs: foo.c and two headers.
+    Edge* edge = state.edges_.back();
     ASSERT_EQ(3u, edge->inputs_.size());
 
     // Expect the command line we generate to only use the original input.
@@ -3675,8 +3682,8 @@ TEST_F(BuildTest, DyndepBuildDiscoverOutputAndDepfileInput) {
   EXPECT_TRUE(builder_.AddTarget("out", &err));
   ASSERT_EQ("", err);
 
-  // Loading the depfile gave tmp.imp a phony input edge.
-  ASSERT_TRUE(GetNode("tmp.imp")->in_edge()->is_phony());
+  // Loading the depfile did not give tmp.imp a phony input edge.
+  ASSERT_FALSE(GetNode("tmp.imp")->in_edge());
 
   EXPECT_TRUE(builder_.Build(&err));
   EXPECT_EQ("", err);
diff --git a/src/dyndep.cc b/src/dyndep.cc
index dd4ed099a9..a0d699d5db 100644
--- a/src/dyndep.cc
+++ b/src/dyndep.cc
@@ -97,15 +97,10 @@ bool DyndepLoader::UpdateEdge(Edge* edge, Dyndeps const* dyndeps,
   for (std::vector<Node*>::const_iterator i =
            dyndeps->implicit_outputs_.begin();
        i != dyndeps->implicit_outputs_.end(); ++i) {
-    if (Edge* old_in_edge = (*i)->in_edge()) {
-      // This node already has an edge producing it.  Fail with an error
-      // unless the edge was generated by ImplicitDepLoader, in which
-      // case we can replace it with the now-known real producer.
-      if (!old_in_edge->generated_by_dep_loader_) {
-        *err = "multiple rules generate " + (*i)->path();
-        return false;
-      }
-      old_in_edge->outputs_.clear();
+    if ((*i)->in_edge()) {
+      // This node already has an edge producing it.
+      *err = "multiple rules generate " + (*i)->path();
+      return false;
     }
     (*i)->set_in_edge(edge);
   }
diff --git a/src/graph.cc b/src/graph.cc
index 199294d481..62f13ec100 100644
--- a/src/graph.cc
+++ b/src/graph.cc
@@ -728,7 +728,6 @@ bool ImplicitDepLoader::ProcessDepfileDeps(
     Node* node = state_->GetNode(*i, slash_bits);
     *implicit_dep = node;
     node->AddOutEdge(edge);
-    CreatePhonyInEdge(node);
   }
 
   return true;
@@ -756,7 +755,6 @@ bool ImplicitDepLoader::LoadDepsFromLog(Edge* edge, string* err) {
     Node* node = deps->nodes[i];
     *implicit_dep = node;
     node->AddOutEdge(edge);
-    CreatePhonyInEdge(node);
   }
   return true;
 }
@@ -768,21 +766,3 @@ vector<Node*>::iterator ImplicitDepLoader::PreallocateSpace(Edge* edge,
   edge->implicit_deps_ += count;
   return edge->inputs_.end() - edge->order_only_deps_ - count;
 }
-
-void ImplicitDepLoader::CreatePhonyInEdge(Node* node) {
-  if (node->in_edge())
-    return;
-
-  Edge* phony_edge = state_->AddEdge(&State::kPhonyRule);
-  phony_edge->generated_by_dep_loader_ = true;
-  node->set_in_edge(phony_edge);
-  phony_edge->outputs_.push_back(node);
-
-  // RecomputeDirty might not be called for phony_edge if a previous call
-  // to RecomputeDirty had caused the file to be stat'ed.  Because previous
-  // invocations of RecomputeDirty would have seen this node without an
-  // input edge (and therefore ready), we have to set outputs_ready_ to true
-  // to avoid a potential stuck build.  If we do call RecomputeDirty for
-  // this node, it will simply set outputs_ready_ to the correct value.
-  phony_edge->outputs_ready_ = true;
-}
diff --git a/src/graph.h b/src/graph.h
index d07a9b7639..5c8ca2c610 100644
--- a/src/graph.h
+++ b/src/graph.h
@@ -104,6 +104,14 @@ struct Node {
   Edge* in_edge() const { return in_edge_; }
   void set_in_edge(Edge* edge) { in_edge_ = edge; }
 
+  /// Indicates whether this node was generated from a depfile or dyndep file,
+  /// instead of being a regular input or output from the Ninja manifest.
+  bool generated_by_dep_loader() const { return generated_by_dep_loader_; }
+
+  void set_generated_by_dep_loader(bool value) {
+    generated_by_dep_loader_ = value;
+  }
+
   int id() const { return id_; }
   void set_id(int id) { id_ = id; }
 
@@ -146,6 +154,13 @@ struct Node {
   /// has not yet been loaded.
   bool dyndep_pending_;
 
+  /// Set to true when this node comes from a depfile, a dyndep file or the
+  /// deps log. If it does not have a producing edge, the build should not
+  /// abort if it is missing (as for regular source inputs). By default
+  /// all nodes have this flag set to true, since the deps and build logs
+  /// can be loaded before the manifest.
+  bool generated_by_dep_loader_ = true;
+
   /// The Edge that produces this Node, or NULL when there is no
   /// known edge to produce it.
   Edge* in_edge_;
@@ -297,11 +312,6 @@ struct ImplicitDepLoader {
   /// an iterator pointing at the first new space.
   std::vector<Node*>::iterator PreallocateSpace(Edge* edge, int count);
 
-  /// If we don't have a edge that generates this input already,
-  /// create one; this makes us not abort if the input is missing,
-  /// but instead will rebuild in that circumstance.
-  void CreatePhonyInEdge(Node* node);
-
   State* state_;
   DiskInterface* disk_interface_;
   DepsLog* deps_log_;
diff --git a/src/manifest_parser.cc b/src/manifest_parser.cc
index 8db6eb3009..103c365ebf 100644
--- a/src/manifest_parser.cc
+++ b/src/manifest_parser.cc
@@ -14,8 +14,10 @@
 
 #include "manifest_parser.h"
 
+#include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
+
 #include <vector>
 
 #include "graph.h"
@@ -416,6 +418,7 @@ bool ManifestParser::ParseEdge(string* err) {
     if (dgi == edge->inputs_.end()) {
       return lexer_.Error("dyndep '" + dyndep + "' is not an input", err);
     }
+    assert(!edge->dyndep_->generated_by_dep_loader());
   }
 
   return true;
diff --git a/src/state.cc b/src/state.cc
index 556b0d8802..0a68f2163a 100644
--- a/src/state.cc
+++ b/src/state.cc
@@ -128,6 +128,7 @@ Node* State::SpellcheckNode(const string& path) {
 
 void State::AddIn(Edge* edge, StringPiece path, uint64_t slash_bits) {
   Node* node = GetNode(path, slash_bits);
+  node->set_generated_by_dep_loader(false);
   edge->inputs_.push_back(node);
   node->AddOutEdge(edge);
 }
@@ -138,6 +139,7 @@ bool State::AddOut(Edge* edge, StringPiece path, uint64_t slash_bits) {
     return false;
   edge->outputs_.push_back(node);
   node->set_in_edge(edge);
+  node->set_generated_by_dep_loader(false);
   return true;
 }
 
@@ -145,6 +147,7 @@ void State::AddValidation(Edge* edge, StringPiece path, uint64_t slash_bits) {
   Node* node = GetNode(path, slash_bits);
   edge->validations_.push_back(node);
   node->AddValidationOutEdge(edge);
+  node->set_generated_by_dep_loader(false);
 }
 
 bool State::AddDefault(StringPiece path, string* err) {
diff --git a/src/state.h b/src/state.h
index 878ac6d991..886b78f765 100644
--- a/src/state.h
+++ b/src/state.h
@@ -105,6 +105,9 @@ struct State {
   Node* LookupNode(StringPiece path) const;
   Node* SpellcheckNode(const std::string& path);
 
+  /// Add input / output / validation nodes to a given edge. This also
+  /// ensures that the generated_by_dep_loader() flag for all these nodes
+  /// is set to false, to indicate that they come from the input manifest.
   void AddIn(Edge* edge, StringPiece path, uint64_t slash_bits);
   bool AddOut(Edge* edge, StringPiece path, uint64_t slash_bits);
   void AddValidation(Edge* edge, StringPiece path, uint64_t slash_bits);