Layered monorepo_root overlays trigger monorepo_auto_discovery warning

[airtonix]

Summary

With mise 2026.9.3, layered environment config files that each set monorepo_root = true cause mise to emit the deprecated monorepo_auto_discovery warning, even when the canonical root mise.toml has explicit [monorepo].config_roots.

The monorepo task still runs successfully, but the warning is unexpected because automatic discovery should not be needed.

Reproduction

https://gist.github.com/airtonix/6c61883d5ca7bd527bf0adeee34d7d5f

/tmp/mise-monorepo-repro-all/
├── mise.toml
├── mise.unix.toml
├── mise.linux.toml
└── projects/child/mise.toml

mise.toml:

monorepo_root = true

[monorepo]
config_roots = ["projects/child"]

mise.unix.toml:

monorepo_root = true

[env]
REPRO_PLATFORM = "unix"

mise.linux.toml:

monorepo_root = true

[env]
REPRO_PLATFORM = "linux"

projects/child/mise.toml:

[tasks.hello]
description = "Minimal monorepo task"
run = "printf 'hello from child\\n'"

On Linux:

$ mise --version
2026.9.3 linux-x64 (2026-09-08)

$ mise -C /tmp/mise-monorepo-repro-all run //projects/child:hello
mise WARN  deprecated [monorepo_auto_discovery]: Automatic monorepo discovery is deprecated. Please define [monorepo].config_roots in your root mise.toml.
[//projects/child:hello] $ printf 'hello from child\\n'
hello from child

Control

Removing monorepo_root = true from both environment files makes the warning disappear in an equivalent minimal setup:

mise.toml                 -> monorepo_root = true + [monorepo].config_roots
mise.unix.toml            -> [env] only
mise.linux.toml           -> [env] only

The same command then runs without the warning:

$ mise -C /tmp/mise-monorepo-repro-root-only run //projects/child:hello
[//projects/child:hello] $ printf 'hello from child\\n'
hello from child

In the larger repository that prompted this report, removing the overlay declarations causes monorepo task paths to fail instead, so the behavior may depend on how mise selects the active monorepo root from layered configs.

Expected behavior

A single canonical root mise.toml with explicit [monorepo].config_roots should be sufficient. Platform overlays should be able to contain environment-specific settings without triggering automatic discovery or changing monorepo root selection.

Additional context

The warning repeats when tasks invoke nested mise run commands. The separate [bootstrap].config_roots setting is not involved; it controls bootstrap resources, not monorepo task discovery.

[pchrysostomou]

The overlays are winning the root pick. mise takes the first config in scope with monorepo_root = true and reads [monorepo].config_roots only from that file; within one directory the env overlays sit before mise.toml, so mise.linux.toml gets selected, it has no [monorepo] table, and mise falls back to the deprecated walk (https://github.com/jdx/mise/blob/cb484f06cf3a1c0bb1aa8b53af7d03ee3e5aee5e/src/config/mod.rs#L1739-L1743; the read is at L4172-L4176). Fix: set monorepo_root = true in mise.toml only, or put the same [monorepo].config_roots in every overlay that sets it. Reproduced on 2026.9.5 with your gist: both variants clear the warning. The [monorepo] table isn't merged across layered files, which is probably worth an issue.

[jdx]

Thanks for the diagnosis. This is a bug in how mise resolves same-directory config layers: the nearest-root rule is meant to choose between directories, but the implementation was accidentally choosing one physical config file and reading [monorepo] only from it.

I opened #13084 to resolve the root at the directory level and merge its active config layers. An omitted config_roots inherits the lower-precedence value; if an overlay defines config_roots, its list replaces the lower-precedence list. The change also preserves nested/worktree root selection and lets an explicit higher-precedence monorepo_root = false disable the root.

AI-assisted — Tool: Codex; model: openai/gpt-5; version: unavailable.