Do not touch sources when external resources change

Instead we store the changed files in the checkpoint.

This also address an issue where Elixir would say
"mtime was set in the future" when compiled too quickly.

See 7d521de. Closes #15277.

Author: josevalim

lib/mix/lib/mix/compilers/elixir.ex

@@ -6,7 +6,7 @@ defmodule Mix.Compilers.Elixir do
   @moduledoc false
 
   @manifest_vsn 34
-  @checkpoint_vsn 4
+  @checkpoint_vsn 5
 
   import Record
 
@@ -163,8 +163,7 @@ defmodule Mix.Compilers.Elixir do
           removed,
           Map.merge(stale_modules, removed_modules),
           Map.merge(stale_exports, removed_modules),
-          dest,
-          timestamp
+          dest
         )
       end
 
@@ -387,36 +386,17 @@ defmodule Mix.Compilers.Elixir do
          removed,
          stale_modules,
          stale_exports,
-         dest,
-         timestamp
+         dest
        ) do
-    {checkpoint_stale_modules, checkpoint_stale_exports} =
+    {checkpoint_stale_modules, checkpoint_stale_exports, checkpoint_changed} =
       case parse_checkpoint(:update, manifest) do
-        {:ok, {_, _} = data} -> data
-        :error -> {%{}, %{}}
+        {:ok, {_, _, _} = data} -> data
+        :error -> {%{}, %{}, %{}}
       end
 
     stale_modules = Map.merge(checkpoint_stale_modules, stale_modules)
     stale_exports = Map.merge(checkpoint_stale_exports, stale_exports)
 
-    # Once we added semantic recompilation, the following can happen:
-    #
-    # 1. The user changes config/mix.exs/__mix_recompile__?
-    # 2. We detect the change, remove .beam files and start recompilation
-    # 3. Recompilation fails
-    # 4. The user reverts the change
-    # 5. The compiler no longer recompiles and the .beam files are missing
-    #
-    # Therefore, it is important for us to checkpoint any state that may
-    # have lead to a compilation and which can now be reverted.
-    if map_size(stale_modules) != map_size(checkpoint_stale_modules) or
-         map_size(stale_exports) != map_size(checkpoint_stale_exports) do
-      write_checkpoint(:update, manifest, {stale_modules, stale_exports})
-    end
-
-    # We don't need to store those in the checkpoint because
-    # these changes come from modules and, when they are stale,
-    # we remove the .beam files and touch sources.
     modules_to_mix_check =
       for {module, module(recompile?: true)} <- all_modules,
           not Map.has_key?(stale_modules, module),
@@ -448,33 +428,45 @@ defmodule Mix.Compilers.Elixir do
     # Sources that have changed on disk or
     # any modules associated with them need to be recompiled
     changed =
-      Enum.flat_map(all_sources, fn
+      Enum.reduce(all_sources, checkpoint_changed, fn
         {source,
-         source(external: external, size: size, mtime: mtime, digest: digest, modules: modules)} ->
+         source(external: external, size: size, mtime: mtime, digest: digest, modules: modules)},
+        acc ->
           {last_mtime, last_size} = Map.fetch!(sources_stats, source)
 
           cond do
             Enum.any?(external, &stale_external?(&1, sources_stats)) or
                 has_any_key?(modules_to_recompile, modules) ->
-              # Mark the source as changed so the combination of a timestamp
-              # plus removed beam files (which are removed by update_stale_entries)
-              # causes it to be recompiled. Note we don't raise use touch! because
-              # in case of checkpoints the file may have been removed.
-              File.touch(source, timestamp + 1)
-              [source]
+              Map.put(acc, source, true)
 
             size != last_size or
               has_any_key?(stale_modules, modules) or
                 (last_mtime != mtime and
                    (missing_beam_file?(dest, modules) or digest_changed?(source, digest))) ->
-              [source]
+              Map.put(acc, source, true)
 
             true ->
-              []
+              acc
           end
       end)
 
-    changed = new_paths ++ changed
+    # Once we added semantic recompilation, the following can happen:
+    #
+    # 1. The user changes config/mix.exs/__mix_recompile__?
+    # 2. We detect the change, remove .beam files and start recompilation
+    # 3. Recompilation fails
+    # 4. The user reverts the change
+    # 5. The compiler no longer recompiles and the .beam files are missing
+    #
+    # Therefore, it is important for us to checkpoint any state that may
+    # have lead to a compilation and which can now be reverted.
+    if map_size(stale_modules) != map_size(checkpoint_stale_modules) or
+         map_size(stale_exports) != map_size(checkpoint_stale_exports) or
+         map_size(changed) != map_size(checkpoint_changed) do
+      write_checkpoint(:update, manifest, {stale_modules, stale_exports, changed})
+    end
+
+    changed = new_paths ++ Map.keys(changed)
 
     {modules, exports, changed} =
       update_stale_entries(