docs(config): mark env_file setting deprecated

[risu729]

Summary

• mark the env_file setting metadata as deprecated in settings.toml with a future warning/removal window
• regenerate schema/mise.json so settings.env_file gets the JSON Schema deprecated keyword
• update manual docs to point users at top-level [env] with _.file instead of MISE_ENV_FILE
• update the hidden deprecated profile setting guidance so it no longer points at MISE_ENV_FILE

Tests

• mise run render:schema
• git diff --check
• cargo fmt --check
• cargo test --all-features config::settings::tests::test_settings_toml_is_sorted
• mise run docs:build
• mise run test:e2e config/test_schema_tombi

This PR was generated by an AI coding assistant.

[gemini-code-assist]

Code Review

This pull request deprecates the env_file configuration setting and the MISE_ENV_FILE environment variable in favor of env._.file. The changes include updates to the documentation, JSON schema, and settings configuration to mark these features as deprecated and establish a timeline for their eventual removal. I have no feedback to provide as there were no review comments.

[greptile-apps]

Greptile Summary

This PR marks env_file / MISE_ENV_FILE as deprecated in favour of the [env] _.file config key, updating the settings metadata, JSON Schema, and documentation to guide users toward the replacement.

• settings.toml: adds deprecated, deprecated_warn_at = \"2026.11.0\", and deprecated_remove_at = \"2027.11.0\" to [env_file]; fixes the chained deprecation on [profile] that previously pointed users at the now-deprecated MISE_ENV_FILE.
• schema/mise.json: regenerated to include \"deprecated\": true on env_file (valid in JSON Schema draft 2020-12).
• Docs: replaces the env_file = '.env' setting example with [env] _.file = '.env' and adds a deprecation notice to the MISE_ENV_FILE reference page.

Confidence Score: 5/5

Safe to merge — purely additive deprecation metadata with no behavioural changes to the runtime.

The change only adds deprecation markers and updates documentation. The deprecated_warn_at date (2026.11.0) is in the future, giving users a comfortable migration window. The chained deprecation message in [profile] has been corrected to point directly to env._.file. No runtime logic is altered.

No files require special attention.

Important Files Changed

Filename	Overview
settings.toml	Adds deprecation metadata to [env_file]; fixes chained deprecation message in [profile] to point directly to env._.file
schema/mise.json	Adds "deprecated": true to the env_file property; schema uses draft 2020-12 which supports this annotation keyword natively
docs/configuration.md	Replaces env_file = '.env' example with [env] _.file = '.env'; adds deprecation notice above the MISE_ENV_FILE env var section
docs/environments/index.md	Updates prose to label MISE_ENV_FILE as legacy/deprecated and directs users to env._.file

_{Reviews (2): Last reviewed commit: "docs(config): fix env_file deprecation g..." | Re-trigger Greptile}

[risu729]

CI is green except for benchmark. I checked the failed job log: the failure is the perf threshold for mise ls (mise-2026.5.7 ls 16.0 ms vs this branch 18.6 ms, reported as 16% variance). This PR only changes settings metadata, generated schema, and docs, so I am treating that benchmark failure as unrelated to this change.

The Greptile feedback about the past deprecated_warn_at date and [profile] pointing at MISE_ENV_FILE was addressed in 87a3d92.

This comment was generated by an AI coding assistant.