Fix JLL version fix fix

[IanButterworth]

Reported here JuliaRegistries/General#122129 (comment)

ERROR: KeyError: key v"1.0.11+3" not found
Stacktrace:
  [1] getindex
    @ ./dict.jl:498 [inlined]
  [2] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber, installed_only::Bool)
    @ Pkg.Operations ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:452
  [3] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, level::Pkg.Types.UpgradeLevel; skip_writing_project::Bool, preserve::Nothing)
    @ Pkg.Operations ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1546
  [4] up
    @ ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1528 [inlined]
  [5] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; level::Pkg.Types.UpgradeLevel, mode::Pkg.Types.PackageMode, preserve::Nothing, update_registry::Bool, skip_writing_project::Bool, kwargs::@Kwargs{})
    @ Pkg.API ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/API.jl:351
  [6] up
    @ ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/API.jl:326 [inlined]
  [7] up
    @ ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/API.jl:164 [inlined]
  [8] #resolve#143
    @ ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/API.jl:357 [inlined]
  [9] resolve
    @ ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/API.jl:356 [inlined]
 [10] resolve(; io::Base.TTY, kwargs::@Kwargs{})
    @ Pkg.API ~/.asdf/installs/julia/1.10.7/share/julia/stdlib/v1.10/Pkg/src/API.jl:355
 [11] top-level scope
    @ none:1

[IanButterworth]

I don't understand why currently but this bug only happens when the JLLs are in the sysimage

[IanButterworth]

Maybe this shouldn't be deleted, for cases where the package version in Project.toml and the manifest don't match, and the package is in the sysimage. i.e. #4131

[IanButterworth]

@KristofferC do you think this delete! should be here? I'm leaning towards no to be safer in case I haven't thought through all situations, but not sure

[IanButterworth]

I've removed it with a comment

[IanButterworth]

Tested and appears to work.
With a sysimage with Xorg_libXau_jll v1.0.11+3 in it (which has a version in its Project.toml of v1.0.11+1)

Master

% ./julia --sysimage=JLLTestSysimage.so --project=jll_test
               _
   _       _ _(_)_     |  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)
|__/                   |

(jll_test) pkg> st
Status `~/Documents/GitHub/julia/jll_test/Project.toml`
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+3

(jll_test) pkg> add Example
   Resolving package versions...
ERROR: KeyError: key v"1.0.11+3" not found
Stacktrace:
  [1] getindex
    @ ./dict.jl:477 [inlined]
  [2] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber, installed_only::Bool)
    @ Pkg.Operations ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:539
  [3] targeted_resolve(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
    @ Pkg.Operations ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1607
  [4] tiered_resolve(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber, try_all_installed::Bool)
    @ Pkg.Operations ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1572
  [5] _resolve(io::IOContext{IO}, env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
    @ Pkg.Operations ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1615
  [6] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; allow_autoprecomp::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol)
    @ Pkg.Operations ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1651
  [7] add
    @ ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1623 [inlined]
  [8] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{io::IOContext{IO}})
    @ Pkg.API ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:317
  [9] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{})
    @ Pkg.API ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:164
 [10] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:153
 [11] do_cmd(command::Pkg.REPLMode.Command, io::Base.TTY)
    @ Pkg.REPLMode ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/REPLMode/REPLMode.jl:409
 [12] do_cmds(commands::Vector{Pkg.REPLMode.Command}, io::Base.TTY)
    @ Pkg.REPLMode ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/src/REPLMode/REPLMode.jl:395
 [13] do_cmds(repl::REPL.LineEditREPL, commands::String)
    @ REPLExt ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/ext/REPLExt/REPLExt.jl:99
 [14] on_done(s::REPL.LineEdit.MIState, buf::IOBuffer, ok::Bool, repl::REPL.LineEditREPL)
    @ REPLExt ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/ext/REPLExt/REPLExt.jl:113
 [15] #invokelatest#1
    @ ./essentials.jl:1056 [inlined]
 [16] invokelatest
    @ ./essentials.jl:1052 [inlined]
 [17] (::REPLExt.var"#create_mode##0#create_mode##1"{REPL.LineEditREPL})(s::REPL.LineEdit.MIState, buf::IOBuffer, ok::Bool)
    @ REPLExt ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/Pkg/ext/REPLExt/REPLExt.jl:135
 [18] #invokelatest#1
    @ ./essentials.jl:1056 [inlined]
 [19] invokelatest
    @ ./essentials.jl:1052 [inlined]
 [20] run_interface(terminal::REPL.Terminals.TextTerminal, m::REPL.LineEdit.ModalInterface, s::REPL.LineEdit.MIState)
    @ REPL.LineEdit ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:2800
 [21] run_frontend(repl::REPL.LineEditREPL, backend::REPL.REPLBackendRef)
    @ REPL ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:1681
 [22] (::REPL.var"#59#60"{REPL.LineEditREPL, REPL.REPLBackendRef})()
    @ REPL ~/Documents/GitHub/julia/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:687

This PR

% ./julia --sysimage=JLLTestSysimage.so --project=../Pkg.jl -ie "using Pkg"
[ Info: Precompiling Pkg [44cfe95a-1eb2-52ea-b672-e2afdf69b78f] (cache misses: wrong source (1), mismatched flags (2), wrong julia version (1))
[ Info: Precompiling REPLExt [e5eb5ef1-03cf-53a7-ae1d-5a66b08e832b] (cache misses: wrong dep version loaded (1), mismatched flags (1), wrong julia version (1))
               _
   _       _ _(_)_     |  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)
|__/                   |

(Pkg) pkg> activate jll_test
  Activating project at `~/Documents/GitHub/julia/jll_test`

(jll_test) pkg> st
Status `~/Documents/GitHub/julia/jll_test/Project.toml`
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+3

(jll_test) pkg> add Example
   Resolving package versions...
    Updating `~/Documents/GitHub/julia/jll_test/Project.toml`
  [7876af07] + Example v0.5.5
    Updating `~/Documents/GitHub/julia/jll_test/Manifest.toml`
  [7876af07] + Example v0.5.5
Precompiling packages finished.
  1 dependency successfully precompiled in 1 seconds

(jll_test) pkg> st
Status `~/Documents/GitHub/julia/jll_test/Project.toml`
  [7876af07] Example v0.5.5
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+3

[KristofferC]

Makes sense to me. I wonder how hard it would be to make a test.

[IanButterworth]

I wonder how hard it would be to make a test.

If there was a stdlib JLL that's marked as upgradable, I think we could do a test relatively easily. That's not the case, I believe?

But without that it'd require PackageCompiler which would take time and need manual installation over on julia CI because test deps aren't automatically installed there.