Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request enhances the mise doctor command by introducing a new diagnostic check for PATH environment variable ordering. The purpose is to proactively identify and inform users about configurations where mise-managed tools might be shadowed by other system-installed tools due to incorrect PATH sequencing. This ensures that mise operates as expected when activated, improving the reliability and user experience by guiding them to correct their shell configurations.

Highlights

• New Doctor Check: Added a new check to mise doctor to detect issues with the PATH environment variable ordering.
• PATH Ordering Warning: The check warns users when non-mise paths precede mise tool paths, which could lead to system tools shadowing mise-managed versions.
• Activation Context: This warning is only triggered when mise is actively activated, not for shims-only setups.
• Actionable Feedback: The warning message lists the specific paths that take precedence, helping users identify and fix the configuration issue.

Greptile Summary

This PR adds a check_path_ordering diagnostic to mise doctor that warns when the user is running with mise activate but non-mise paths appear before mise-managed tool paths in PATH. It is integrated into both the text (doctor) and JSON (doctor_json) output paths, and the e2e test suite is extended with before/after assertions.

Key changes:

• New check_path_ordering async method on Doctor in src/cli/doctor/mod.rs (lines 484–550): uses ts.final_env + ts.list_final_paths to build the complete set of mise-managed paths (tool installs, env._.path, UV venv, MISE_ADD_PATH), then compares against PATH_NON_PRISTINE to find the first mise path and warn about anything preceding it.
• The mise binary's own parent directory (e.g. /opt/homebrew/bin) is correctly excluded from the warning via a canonicalized mise_bin_parent comparison, preventing false positives for the common Homebrew install layout.
• check_path_ordering is correctly wired into both doctor_json (line 123) and analyze_config → doctor (line 336).
• E2e test (e2e/cli/test_doctor) adds three assertions: no warning with a clean PATH, warning appears when a fake path is prepended, and the fake path appears in the warning text.

Minor observations:

• The comment on lines 523–524 ("already covered by the activation check") is inaccurate — is_activated() only checks __MISE_DIFF, not whether mise paths are actually present in PATH.
• The resolve closure is called twice for paths in current_path[..first_mise_idx] (once during position(), once in the filter()), causing duplicate canonicalize syscalls for the same entries.
• The e2e test's non-existent /tmp/fake-system-bin directory works correctly via the canonicalize fallback but would benefit from a clarifying comment.

Confidence Score: 4/5

• Safe to merge — the new diagnostic is read-only and additive; no install or execution behavior is changed.
• The implementation correctly uses list_final_paths (covering all mise-managed path categories including env._.path, UV venv, and MISE_ADD_PATH) and properly canonicalizes mise_bin_parent before comparison. The is_activated() guard ensures the check is skipped for shims-only setups. The remaining issues are minor: a slightly inaccurate comment in the early-return branch and duplicate canonicalize calls for the prefix slice. No correctness, security, or data-integrity risks were identified in the new code.
• No files require special attention — both changed files are low-risk additions.

Important Files Changed

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[mise doctor / mise doctor --json] --> B{is_activated?\n__MISE_DIFF set?}
    B -- No --> Z[Skip check]
    B -- Yes --> C[ts.final_env config\nget EnvResults]
    C -- Err --> Z
    C -- Ok --> D[ts.list_final_paths config env_results\nenv._.path + UV venv + MISE_ADD_PATH + tool paths]
    D -- Err --> Z
    D -- Ok, empty --> Z
    D -- Ok, non-empty --> E[Read PATH_NON_PRISTINE\ncurrent process PATH]
    E -- empty --> Z
    E -- non-empty --> F[Build mise_paths_resolved HashSet\ncanonicalised]
    F --> G[Canonicalize MISE_BIN.parent\nmise_bin_parent]
    G --> H[position: first PATH entry\nin mise_paths_resolved]
    H -- None --> Z
    H -- idx == 0 --> Z
    H -- idx > 0 --> I[Filter PATH 0..idx\nexclude mise_bin_parent]
    I -- empty after filter --> Z
    I -- non-empty --> J[Push warning\nmise tool paths are not first in PATH\nlist offending paths]
    J --> K[Warning shown in\ndoctor output / JSON]

_{Last reviewed commit: 0fdfc22}

bugbot run

Hyperfine Performance

mise x -- echo

mise env

mise hook-env

mise ls

xtasks/test/perf

Looks like the tests failed, it looks like a temporary issue that might be fixed with a retry?

If not, I can fork the repo and branch and see if I can fix it from there?

Appreciate you doing this!