Develop can create an incorrect Manifest; moves weakdeps to deps

[kmp5VT]

Hi I reported this problem on the julia discourse and this is a repost here because I think its actually a bug see
https://discourse.julialang.org/t/does-pkg-develop-have-different-behavior-with-and-without-path/101325

I am having an interesting issue with the Package manager system and wondering if its related to the way my Project.toml is set up. The issue is that when I call Pkg.develop with and without a path to a project in .julia/dev two different Manifest.toml are instantiated. One seems to have an error where Pkg is not properly creating a weakdeps section. Here is my julia info

Julia Version 1.9.2
Commit e4ee485e909 (2023-07-05 09:39 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 32 × Intel(R) Xeon(R) Gold 6244 CPU @ 3.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, cascadelake)
  Threads: 1 on 32 virtual cores
Environment:
  LD_LIBRARY_PATH = /mnt/sw/nix/store/wxp5xscxcqq0l1nlrv8k136qs5wqaln6-vscode-1.73.1/lib:/mnt/sw/nix/store/hayjz1l94cb2ky37bhcv71aygjzq7fci-openblas-0.3.21/lib:/cm/shared/apps/slurm/current/lib64:/run/opengl-driver/lib

I installed julia using juliaup and am using juliaup default release

Here is the project.toml

name = "NDTensors"
uuid = "23ae76d9-e61a-49c4-8f12-3f1a16adf9cf"
authors = ["Matthew Fishman <mfishman@flatironinstitute.org>"]
version = "0.2.0"

[deps]
somedeps = "UUID"

[compat]
somedeps = "version#"

[weakdeps]
CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"

[extensions]
NDTensorCUDA = "CUDA"

The issue happens when I try to dev my project so I have the folder .julia/dev/NDTensors and cd to .julia/dev. When I run this command $julia --project=temp -e 'using Pkg; Pkg.develop(path="./NDTensors")' or this $julia --project=temp -e 'using Pkg; Pkg.develop(path="NDTensors")' I get this error

Resolving package versions...
ERROR: `NDTensors=23ae76d9-e61a-49c4-8f12-3f1a16adf9cf` depends on `CUDA=052768ef-5323-5732-b1bb-66c8b64840ba`, but no such entry exists in the manifest.
and Pkg has created a manifest (temp/Manifest.toml) that looks like this
[[deps.NDTensors]]
path = "../NDTensors"
uuid = "23ae76d9-e61a-49c4-8f12-3f1a16adf9cf"
version = "0.2.0"

    [deps.NDTensors.deps]
    somedeps = "UUID"
    CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"

which looks like Pkg has incorrectly put my weakdeps in deps. However if I run this command $julia --project=temp -e 'using Pkg; Pkg.develop("NDTensors") Pkg generates this manifest

[[deps.NDTensors]]
deps = ["somedeps"]
path = "/home/.julia/dev/NDTensors"
uuid = "23ae76d9-e61a-49c4-8f12-3f1a16adf9cf"
version = "0.2.0"

    [deps.NDTensors.extensions]
    NDTensorCUDA = "CUDA"

    [deps.NDTensors.weakdeps]
    CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"

[IanButterworth]

I wonder if this is related to #3327 given I saw it when dev-ing

[evetion]

Just hit this as well in testing for GeoInterface, in which the common design for testing subpackages does a julia --project=monorepo, and than devs all (sub)packages.

I also made a new package from scratch to confirm this issue (ofcourse only on 1.9+) as well. Doing a dev with path=("."), converts the weakdep in the package Project.toml to a dep in the Manifest of the project.