JLLs in the sysimage confuse Pkg.update when their Project.toml version build doesn't match the registry build number

[IanButterworth]

Usually JLL build numbers in their Project.toml match the registered build number, but JuliaRegistries/General#122129 was done with the intention of being the least breaking way to undo an awkward compat issue.

This seems to be fine, except if the JLLs are in a sysimage.

Here, it seems Pkg.update thinks the loaded version is +1 (I assume based on pkgorigins) where it's actually +3 in manifest terms (based off the registry).

(@v1.12) pkg> activate jll_test
  Activating new project at `~/Documents/GitHub/julia/jll_test`

(jll_test) pkg> add [email protected]
   Resolving package versions...
    Updating `~/Documents/GitHub/julia/jll_test/Project.toml`
  [0c0b7dd1] + Xorg_libXau_jll v1.0.11+3
    Updating `~/Documents/GitHub/julia/jll_test/Manifest.toml`
  [692b3bcd] + JLLWrappers v1.7.0
  [21216c6a] + Preferences v1.4.3
  [0c0b7dd1] + Xorg_libXau_jll v1.0.11+3
  [56f22d72] + Artifacts v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8f399da3] + Libdl v1.11.0
  [de0858da] + Printf v1.11.0
  [fa267f1f] + TOML v1.0.3
  [4ec0a83e] + Unicode v1.11.0

julia> create_sysimage(["Xorg_libXau_jll"]; sysimage_path="JLLTestSysimage.so")
Precompiling packages finished.
  4 dependencies successfully precompiled in 2 seconds. 3 already precompiled.
✔ [01m:12s] PackageCompiler: compiling incremental system image
ld: warning: reexported library with install name '@rpath/libunwind.1.dylib' found at '/Users/ian/Documents/GitHub/julia/usr/lib/libunwind.1.0.dylib' couldn't be matched with any parent library and will be linked directly

julia>
ian@Ians-MacBook-Pro julia % ./julia --sysimage=JLLTestSysimage.so
Precompiling InteractiveUtils finished.
  5 dependencies successfully precompiled in 11 seconds
Precompiling REPL finished.
  1 dependency successfully precompiled in 22 seconds. 5 already precompiled.
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.12.0-DEV.1869 (2025-01-10)
 _/ |\__'_|_|_|\__'_|  |  Commit d3964b600a (0 days old master)
|__/                   |

julia> import Pkg
Precompiling Pkg finished.
  17 dependencies successfully precompiled in 40 seconds. 4 already precompiled.
Precompiling REPLExt finished.
  1 dependency successfully precompiled in 3 seconds. 23 already precompiled.

(@v1.12) pkg> activate jll_test
  Activating project at `~/Documents/GitHub/julia/jll_test`

(jll_test) pkg> update
    Updating registry at `~/.julia/registries/HolyLabRegistry`
    Updating git-repo `[email protected]:HolyLab/HolyLabRegistry`
    Updating registry at `~/.julia/registries/LeukoRegistry`
    Updating git-repo `[email protected]:LeukoMaster/LeukoRegistry`
    Updating registry at `~/.julia/registries/General.toml`
    Updating `~/Documents/GitHub/julia/jll_test/Project.toml`
⌅ [0c0b7dd1] ↓ Xorg_libXau_jll v1.0.11+3 ⇒ v1.0.11+1
    Updating `~/Documents/GitHub/julia/jll_test/Manifest.toml`
⌅ [0c0b7dd1] ↓ Xorg_libXau_jll v1.0.11+3 ⇒ v1.0.11+1
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

(jll_test) pkg> add [email protected]
   Resolving package versions...
No packages added to or removed from `~/Documents/GitHub/julia/jll_test/Project.toml`
No packages added to or removed from `~/Documents/GitHub/julia/jll_test/Manifest.toml`

(jll_test) pkg>

This is somehow related to the error #4130 tries to fix, but I haven't found a reproducer yet.

cc. @giordano