Automatically upgrade empty manifest files to v2 format

src/manifest.jl

@@ -219,7 +219,11 @@ function read_manifest(f_or_io::Union{String, IO})
         rethrow()
     end
     if Base.is_v1_format_manifest(raw)
-        raw = convert_v1_format_manifest(raw)
+        if isempty(raw) # treat an empty Manifest file as v2 format for convenience
+            raw["manifest_format"] = "2.0.0"
+        else
+            raw = convert_v1_format_manifest(raw)
+        end
     end
     return Manifest(raw, f_or_io)
 end

test/manifests.jl

@@ -44,6 +44,35 @@ end
         end
     end
 
+    @testset "Empty manifest file is automatically upgraded to v2" begin
+        isolate(loaded_depot=true) do
+            io = IOBuffer()
+            d = mktempdir()
+            manifest = joinpath(d, "Manifest.toml")
+            touch(manifest)
+            Pkg.activate(d; io=io)
+            output = String(take!(io))
+            @test occursin(r"Activating.*project at.*", output)
+            env_manifest = Pkg.Types.Context().env.manifest_file
+            @test samefile(env_manifest, manifest)
+            # an empty manifest is still technically considered to be v1 manifest
+            @test Base.is_v1_format_manifest(Base.parsed_toml(env_manifest))
+            @test Pkg.Types.Context().env.manifest.manifest_format == v"2.0.0"
+
+            Pkg.add("Profile"; io=io)
+            env_manifest = Pkg.Types.Context().env.manifest_file
+            @test samefile(env_manifest, manifest)
+            @test Base.is_v1_format_manifest(Base.parsed_toml(env_manifest)) == false
+            @test Pkg.Types.Context().env.manifest.manifest_format == v"2.0.0"
+
+            # check that having a Project with deps, and an empty manifest file doesn't error
+            rm(manifest)
+            touch(manifest)
+            Pkg.activate(d; io=io)
+            Pkg.add("Example"; io=io)
+        end
+    end
+
     @testset "v1.0: activate, change, maintain manifest format" begin
         reference_manifest_isolated_test("v1.0", v1 = true) do env_dir, env_manifest
             io = IOBuffer()