fix(config): restore MISE_ENV_FILE setting

[risu729]

Summary

• remove the deprecation metadata from the env_file setting / MISE_ENV_FILE
• restore global config docs for [settings] env_file = ".env"
• clarify that MISE_ENV_FILE loads all matching files found from the current directory upward, unlike env._.file paths in config files

Context

Discussion: #9897

env._.file is still the right replacement for legacy top-level env_file entries in mise.toml, but it is not a behaviorally equivalent replacement for MISE_ENV_FILE=.env because the setting uses FindUp from the current directory.

Testing

• mise run render:schema
• PR CI passed: docs, lint, Linux/macOS/Windows unit and e2e jobs, nightly, benchmark, registry, release, and Socket checks.
• A local focused e2e run was attempted, but I stopped it after it sat behind shared Cargo build contention for ~19 minutes; the PR CI covered those paths.

This pull request was generated by an AI coding assistant.

[greptile-apps]

Greptile Summary

This PR restores env_file / MISE_ENV_FILE as a first-class (non-deprecated) setting, clarifying that it uses FindUp semantics (loads matching files from the current directory upward) rather than config-file-relative resolution like env._.file.

• settings.toml: Deprecation fields (deprecated, deprecated_warn_at, deprecated_remove_at) removed from [env_file]; [profile]'s deprecation message is updated but still references the wrong env var (MISE_ENV instead of MISE_PROFILE).
• docs/: MISE_ENV_FILE deprecation notice removed in configuration.md; environments/index.md updated to present MISE_ENV_FILE / [settings] env_file as the recommended approach for FindUp dotenv loading.
• schema/mise.json: \"deprecated\": true removed from the env_file entry, consistent with the restored status.

Confidence Score: 4/5

The env_file restoration is correct and well-executed; a stale incorrect deprecation message on the unrelated profile setting will mislead users who encounter that warning.

The profile setting's deprecation message was changed to "Use MISE_ENV instead.", but MISE_ENV is unrelated to profile config files — the setting's own env field already documents MISE_PROFILE as the correct env var. A user who sees this deprecation warning and follows it will configure the wrong thing.

settings.toml — the [profile] deprecation message points to the wrong replacement.

Important Files Changed

Filename	Overview
settings.toml	Removes deprecation metadata from env_file (correct); profile's new deprecation message "Use MISE_ENV instead." points to the wrong env var — the setting already reads from MISE_PROFILE, not MISE_ENV.
docs/configuration.md	Removes deprecation notice for MISE_ENV_FILE, adds FindUp clarification, swaps the global-config example from [env] _.file to [settings] env_file.
docs/environments/index.md	Replaces deprecation warning with a clear explanation distinguishing MISE_ENV_FILE/env_file (FindUp) from env._.file (config-relative path).
schema/mise.json	Removes "deprecated": true from the env_file schema entry, consistent with restoring the setting.

_{Reviews (3): Last reviewed commit: "docs(config): clarify MISE_ENV_FILE find..." | Re-trigger Greptile}

[gemini-code-assist]

Code Review

This pull request undeprecates the env_file setting, removing related deprecation notices from the schema and configuration files. The review feedback identifies a misleading deprecation message for the profile setting, suggesting MISE_ENV as the correct replacement, and recommends clarifying the documentation to explicitly state that MISE_ENV_FILE loads all matching files found in the directory hierarchy.