consider a package with a rev (but without a source) to not be "tracked" by a registry

src/Operations.jl

@@ -351,7 +351,7 @@ function collect_project(pkg::Union{PackageSpec, Nothing}, path::String)
 end
 
 is_tracking_path(pkg) = pkg.path !== nothing
-is_tracking_repo(pkg) = pkg.repo.source !== nothing
+is_tracking_repo(pkg) = (pkg.repo.source !== nothing || pkg.repo.rev !== nothing)
 is_tracking_registry(pkg) = !is_tracking_path(pkg) && !is_tracking_repo(pkg)
 isfixed(pkg) = !is_tracking_registry(pkg) || pkg.pinned
 

src/Types.jl

@@ -1254,7 +1254,6 @@ function write_env(env::EnvCache; update_undo=true,
             @assert entry.path == path
         end
         if repo != GitRepo()
-            @assert entry.repo.source == repo.source
             if repo.rev !== nothing
                 @assert entry.repo.rev == repo.rev
             end
@@ -1266,7 +1265,8 @@ function write_env(env::EnvCache; update_undo=true,
             if entry.path !== nothing
                 env.project.sources[pkg] = Dict("path" => entry.path)
             elseif entry.repo != GitRepo()
-                d = Dict("url" => entry.repo.source)
+                d = Dict{String, String}()
+                entry.repo.source !== nothing && (d["url"] = entry.repo.source)
                 entry.repo.rev !== nothing && (d["rev"] = entry.repo.rev)
                 entry.repo.subdir !== nothing && (d["subdir"] = entry.repo.subdir)
                 env.project.sources[pkg] = d

test/new.jl

@@ -1358,14 +1358,14 @@ end
             @test length(args) == 1
             @test args[1].path == normpath("C:\\\\Users\\\\test\\\\project")
             @test args[1].subdir === nothing
-            
+
             # Test with forward slashes too
             api, args, opts = first(Pkg.pkg"add C:/Users/test/project")
             @test api == Pkg.add
             @test length(args) == 1
             @test args[1].path == normpath("C:/Users/test/project")
             @test args[1].subdir === nothing
-            
+
             # Test that actual subdir syntax still works with Windows paths
             api, args, opts = first(Pkg.pkg"add C:\\Users\\test\\project:subdir")
             @test api == Pkg.add
@@ -3516,6 +3516,23 @@ end
     end
 end
 
+@testset "test instantiate with sources with only rev" begin
+    isolate() do
+        mktempdir() do dir
+            cp(joinpath(@__DIR__, "test_packages", "sources_only_rev", "Project.toml"), joinpath(dir, "Project.toml"))
+            cd(dir) do
+                with_current_env() do
+                    @test !isfile("Manifest.toml")
+                    Pkg.instantiate()
+                    uuid, info = only(Pkg.dependencies())
+                    @test info.git_revision == "ba3d6704f09330ae973773496a4212f85e0ffe45"
+                    @test info.git_source == "https://github.com/JuliaLang/Example.jl.git"
+                end
+            end
+        end
+    end
+end
+
 @testset "status showing incompatible loaded deps" begin
     cmd = addenv(`$(Base.julia_cmd()) --color=no --startup-file=no -e "
         using Pkg

test/test_packages/sources_only_rev/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+Example = "7876af07-990d-54b4-ab0e-23690620f79a"
+
+[sources]
+Example = {rev = "ba3d6704f09330ae973773496a4212f85e0ffe45"}