1.13 rc1: `free`ing `develop`ed packages erros

[pjaap]

Sorry, if already reported. I could not find a suitable bug report.

In current 1.13 rc1 I get the following problem, given by an MWE on a vanilla 1.13rc1 installation:

free throws an error on custom environments. Here with a random package Runic:

               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.13.0-rc1 (2026-04-27)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org release
|__/                   |

(@v1.13) pkg> generate foo
  Generating  project foo:
    foo/Project.toml
    foo/src/foo.jl

(@v1.13) pkg> activate foo
  Activating project at `/foo`

(foo) pkg> add Runic;
  Installing known registries into `~/.julia`
       Added `General` registry to ~/.julia/registries
   Resolving package versions...
   Installed Preferences ─ v1.5.2
   Installed JuliaSyntax ─ v1.0.2
   Installed Runic ─────── v1.7.0
      Compat entries added for Runic
    Updating `/foo/Project.toml`
  [62bfec6d] + Runic v1.7.0
    Updating `/foo/Manifest.toml`
  [70703baa] + JuliaSyntax v1.0.2
  [21216c6a] + Preferences v1.5.2
  [62bfec6d] + Runic v1.7.0
  [ade2ca70] + Dates v1.11.0
  [de0858da] + Printf v1.11.0
  [fa267f1f] + TOML v1.0.3
  [4ec0a83e] + Unicode v1.11.0
Precompiling Runic finished.
  3 dependencies successfully precompiled in 43 seconds. 4 already precompiled.

(foo) pkg> dev Runic
     Cloning git-repo `https://github.com/fredrikekre/Runic.jl.git`
   Resolving package versions...
    Updating `/foo/Project.toml`
  [62bfec6d] ~ Runic v1.7.0 ⇒ v1.7.0 `~/.julia/dev/Runic`
    Updating `/foo/Manifest.toml`
  [62bfec6d] ~ Runic v1.7.0 ⇒ v1.7.0 `~/.julia/dev/Runic`

(foo) pkg> free Runic
   Resolving package versions...
ERROR: could not find source path for package Runic based on manifest /foo/Manifest.toml

(foo) pkg> add Runic
   Resolving package versions...
ERROR: could not find source path for package Runic based on manifest /foo/Manifest.toml

also adding Runic gives the same error.

This happens in all my research projects with 1.13 and pretty much breaks my workflow.