`resolve` reports "No changes to Manifest.toml" despite changing Manifest.toml

[topolarity]

This seems to happen with updates that do not add / remove direct dependencies.

For example, if I start with two unrelated packages Foo and Bar:

$ cat testenv/Manifest.toml
# This file is machine-generated - editing it directly is not advised

julia_version = "1.10.5"
manifest_format = "2.0"
project_hash = "932500bcfbdcc09cf8ba2c662c200c798350bb5a"

[[deps.Bar]]
path = "../Bar"
uuid = "ed96e9dd-c367-45ab-9d59-befe4c57f37f"
version = "0.1.0"

[[deps.Foo]]
path = "../Foo"
uuid = "9b094d01-e697-4a76-8fe8-871656a862e0"
version = "0.1.0"

Add a dependency on Bar in Foo and then resolve:

$ julia +1.10 --project=testenv -q
(testenv) pkg> resolve
  No Changes to `~/repos/julia/testenv/Project.toml`
  No Changes to `~/repos/julia/testenv/Manifest.toml`

(testenv) pkg> ^D

Things did change though:

$ cat testenv/Manifest.toml
# This file is machine-generated - editing it directly is not advised

julia_version = "1.10.5"
manifest_format = "2.0"
project_hash = "932500bcfbdcc09cf8ba2c662c200c798350bb5a"

[[deps.Bar]]
path = "../Bar"
uuid = "ed96e9dd-c367-45ab-9d59-befe4c57f37f"
version = "0.1.0"

[[deps.Foo]]
deps = ["Bar"]
path = "../Foo"
uuid = "9b094d01-e697-4a76-8fe8-871656a862e0"
version = "0.1.0"

[topolarity]

This can also happen even when adding / removing extensions:

    [deps.Foo.extensions]
    FooBarExt = "Bar"

From a user's point-of-view, an extension is almost another package, so it feels like it should be reported here.

[KristofferC]

Dup of #3066 I think

[KristofferC]

Should have been fixed by #3806