fix(config): migrate deprecated keys passed via --config-set

src/config/user/mod.rs

@@ -527,6 +527,18 @@ impl UserConfig {
     /// (via [`deep_merge_table`]) so sibling keys survive —
     /// `--config-set list.full=true` leaves `list.branches` untouched.
     ///
+    /// Each fragment first runs through the same deprecation migration as a
+    /// config file ([`super::deprecation::migrate_content`] — structural and
+    /// silent rewrites, no `UpdateOnly`), so a deprecated key such as
+    /// `merge.no-ff` is canonicalized to `merge.ff` *before* the fragment is
+    /// parsed and merged, instead of falling through as an unknown field.
+    /// Migrating the fragment
+    /// (not the merged document) keeps layer precedence intact: the
+    /// canonicalized override wins over a lower layer's canonical key, rather
+    /// than colliding with it. The rewrite is silent — there is no file to
+    /// materialize, so the file-scoped "run `wt config update`" warning would
+    /// have nothing to act on.
+    ///
     /// The whole layer degrades as a unit: if any fragment fails to parse, or
     /// the merged result fails to deserialize or validate, every override is
     /// dropped and a [`LoadError::CliOverride`] is recorded, so a bad override
@@ -542,7 +554,11 @@ impl UserConfig {
 
         let base = merged_table.clone();
         for raw in overrides {
-            match raw.parse::<toml::Table>() {
+            // `migrate_content` returns the fragment unchanged when it is not
+            // valid TOML, so the parse below still catches a malformed fragment
+            // and drops the whole layer with an attributed warning.
+            let migrated = super::deprecation::migrate_content(raw);
+            match migrated.parse::<toml::Table>() {
                 Ok(fragment) => deep_merge_table(merged_table, fragment),
                 Err(err) => {
                     warnings.push(LoadError::CliOverride {

src/config/user/tests.rs

@@ -2556,6 +2556,41 @@ fn test_cli_override_validation_failure_drops_layer() {
     assert_eq!(config.list.branches, Some(true)); // base preserved
 }
 
+#[test]
+fn test_cli_override_migrates_deprecated_keys() {
+    // A deprecated key passed via `--config-set` runs through the same
+    // deprecation migration as a config file, so it is canonicalized and takes
+    // effect instead of falling through as an unknown field (which serde
+    // silently drops). The rewrite is silent — there is no file to materialize,
+    // so no deprecation warning is recorded.
+
+    // merge.no-ff = true → merge.ff = false
+    let (table, warnings) = apply_overrides(toml::Table::new(), &["merge.no-ff = true"]);
+    assert!(warnings.is_empty(), "merge.no-ff: {warnings:?}");
+    let config: UserConfig = toml::Value::Table(table).try_into().unwrap();
+    assert_eq!(config.merge.ff, Some(false));
+
+    // switch.no-cd = true → switch.cd = false
+    let (table, warnings) = apply_overrides(toml::Table::new(), &["switch.no-cd = true"]);
+    assert!(warnings.is_empty(), "switch.no-cd: {warnings:?}");
+    let config: UserConfig = toml::Value::Table(table).try_into().unwrap();
+    assert_eq!(config.switch.cd, Some(false));
+}
+
+#[test]
+fn test_cli_override_deprecated_key_wins_over_lower_canonical() {
+    // Each fragment is migrated *before* it is merged, so the canonicalized
+    // override replaces a lower layer's canonical key rather than colliding
+    // with it. (Migrating the merged document instead would leave both
+    // `merge.ff` and `merge.no-ff` present, and the migration would keep the
+    // lower layer's `ff`, silently dropping the override.)
+    let base: toml::Table = "[merge]\nff = true\n".parse().unwrap();
+    let (table, warnings) = apply_overrides(base, &["merge.no-ff = true"]);
+    assert!(warnings.is_empty());
+    let config: UserConfig = toml::Value::Table(table).try_into().unwrap();
+    assert_eq!(config.merge.ff, Some(false)); // override (no-ff=true → ff=false) wins
+}
+
 #[test]
 fn test_cli_override_empty_is_noop() {
     let (table, warnings) = apply_overrides(toml::Table::new(), &[]);

tests/integration_tests/list_config.rs

@@ -579,6 +579,31 @@ fn test_list_config_cli_override_after_subcommand(repo: TestRepo) {
     });
 }
 
+/// A *deprecated* key passed via `--config-set` is run through the same
+/// deprecation migration as a config file (`merge.no-ff` → `merge.ff`), so the
+/// override layer is accepted rather than dropped as unknown. The migration is
+/// silent — an inline override has no file for `wt config update` to rewrite —
+/// so no deprecation or `--config-set` warning appears and `list` runs
+/// normally. (That the migrated value takes effect is covered by the
+/// `apply_cli_overrides` unit tests and
+/// `test_switch_config_set_migrates_deprecated_no_cd`; `list` output does not
+/// reflect a `merge` key.)
+#[rstest]
+fn test_list_config_cli_override_deprecated_key_silently_migrated(repo: TestRepo) {
+    fs::write(repo.test_config_path(), "[list]\nbranches = true\n").unwrap();
+    repo.run_git(&["branch", "feature"]);
+
+    let settings = setup_snapshot_settings(&repo);
+    settings.bind(|| {
+        let mut cmd = wt_command();
+        repo.configure_wt_cmd(&mut cmd);
+        cmd.args(["--config-set", "merge.no-ff = true", "list"])
+            .current_dir(repo.root_path());
+
+        assert_cmd_snapshot!(cmd);
+    });
+}
+
 /// Bad values in non-section fields (projects, skip-*-prompt) must still be
 /// attributed to the file, not to env vars.
 #[rstest]

tests/integration_tests/switch.rs

@@ -6420,6 +6420,24 @@ fn test_switch_no_cd_flag_explicit(repo: TestRepo) {
     );
 }
 
+/// A *deprecated* key passed via `--config-set` is migrated to its canonical
+/// form before it is applied (`switch.no-cd` → `switch.cd`), so it takes effect
+/// end-to-end instead of being dropped as an unknown field. The migrated
+/// `switch.cd = false` suppresses the cd directive, so the output omits the
+/// "Cannot change directory" line a cd-enabled switch prints. The migration is
+/// silent: an inline override has no file for `wt config update` to rewrite, so
+/// no deprecation warning appears.
+#[rstest]
+fn test_switch_config_set_migrates_deprecated_no_cd(repo: TestRepo) {
+    repo.run_git(&["branch", "dep-no-cd"]);
+
+    snapshot_switch(
+        "switch_config_set_migrates_deprecated_no_cd",
+        &repo,
+        &["dep-no-cd", "--config-set", "switch.no-cd = true"],
+    );
+}
+
 /// Test that worktrunk works correctly when `worktree.useRelativePaths` is enabled.
 ///
 /// Git 2.48+ supports `worktree.useRelativePaths`, which stores relative paths in the

tests/snapshots/integration__integration_tests__list_config__list_config_cli_override_deprecated_key_silently_migrated.snap

@@ -0,0 +1,57 @@
+---
+source: tests/integration_tests/list_config.rs
+info:
+  program: wt
+  args:
+    - "--config-set"
+    - merge.no-ff = true
+    - list
+  env:
+    APPDATA: "[TEST_CONFIG_HOME]"
+    CLICOLOR_FORCE: "1"
+    COLUMNS: "500"
+    GIT_AUTHOR_DATE: "2025-01-01T00:00:00Z"
+    GIT_COMMITTER_DATE: "2025-01-01T00:00:00Z"
+    GIT_CONFIG_GLOBAL: "[TEST_GIT_CONFIG]"
+    GIT_CONFIG_SYSTEM: /dev/null
+    GIT_TERMINAL_PROMPT: "0"
+    HOME: "[TEST_HOME]"
+    LANG: C
+    LC_ALL: C
+    LLVM_PROFILE_FILE: "[LLVM_PROFILE_FILE]"
+    MOCK_CONFIG_DIR: "[MOCK_CONFIG_DIR]"
+    OPENCODE_CONFIG_DIR: "[TEST_OPENCODE_CONFIG]"
+    PATH: "[PATH]"
+    TERM: alacritty
+    USERPROFILE: "[TEST_HOME]"
+    WORKTRUNK_APPROVALS_PATH: "[TEST_APPROVALS]"
+    WORKTRUNK_CONFIG_PATH: "[TEST_CONFIG]"
+    WORKTRUNK_SYSTEM_CONFIG_PATH: "[TEST_SYSTEM_CONFIG]"
+    WORKTRUNK_TEST_BASH_INSTALLED: "0"
+    WORKTRUNK_TEST_CLAUDE_INSTALLED: "0"
+    WORKTRUNK_TEST_CODEX_INSTALLED: "0"
+    WORKTRUNK_TEST_DELAYED_STREAM_MS: "-1"
+    WORKTRUNK_TEST_EPOCH: "1735776000"
+    WORKTRUNK_TEST_FISH_INSTALLED: "0"
+    WORKTRUNK_TEST_GEMINI_INSTALLED: "0"
+    WORKTRUNK_TEST_NUSHELL_ENV: "0"
+    WORKTRUNK_TEST_OPENCODE_INSTALLED: "0"
+    WORKTRUNK_TEST_POWERSHELL_ENV: "0"
+    WORKTRUNK_TEST_POWERSHELL_INSTALLED: "0"
+    WORKTRUNK_TEST_SKIP_URL_HEALTH_CHECK: "1"
+    WORKTRUNK_TEST_ZSH_INSTALLED: "0"
+    XDG_CONFIG_HOME: "[TEST_CONFIG_HOME]"
+---
+success: true
+exit_code: 0
+----- stdout -----
+  Branch     Status        HEAD±    main↕  Remote⇅  Path               Commit    Age   Message
+@ main           ^|                           |     .                  05a4a45d  16h   Initial commit
++ feature-a      ↑                 ↑1               ../repo.feature-a  1b87d473  16h   Add feature-a file
++ feature-b      ↑                 ↑1               ../repo.feature-b  f62940fc  16h   Add feature-b file
++ feature-c      ↑                 ↑1               ../repo.feature-c  345c7c93  16h   Add feature-c file
+/ feature       /_                                                     05a4a45d  16h   Initial commit
+
+○ Showing 4 worktrees, 1 branches, 3 ahead
+
+----- stderr -----

tests/snapshots/integration__integration_tests__switch__switch_config_set_migrates_deprecated_no_cd.snap

@@ -0,0 +1,51 @@
+---
+source: tests/integration_tests/switch.rs
+info:
+  program: wt
+  args:
+    - switch
+    - dep-no-cd
+    - "--config-set"
+    - switch.no-cd = true
+  env:
+    APPDATA: "[TEST_CONFIG_HOME]"
+    CLICOLOR_FORCE: "1"
+    COLUMNS: "500"
+    GIT_AUTHOR_DATE: "2025-01-01T00:00:00Z"
+    GIT_COMMITTER_DATE: "2025-01-01T00:00:00Z"
+    GIT_CONFIG_GLOBAL: "[TEST_GIT_CONFIG]"
+    GIT_CONFIG_SYSTEM: /dev/null
+    GIT_TERMINAL_PROMPT: "0"
+    HOME: "[TEST_HOME]"
+    LANG: C
+    LC_ALL: C
+    LLVM_PROFILE_FILE: "[LLVM_PROFILE_FILE]"
+    MOCK_CONFIG_DIR: "[MOCK_CONFIG_DIR]"
+    OPENCODE_CONFIG_DIR: "[TEST_OPENCODE_CONFIG]"
+    PATH: "[PATH]"
+    TERM: alacritty
+    USERPROFILE: "[TEST_HOME]"
+    WORKTRUNK_APPROVALS_PATH: "[TEST_APPROVALS]"
+    WORKTRUNK_CONFIG_PATH: "[TEST_CONFIG]"
+    WORKTRUNK_SYSTEM_CONFIG_PATH: "[TEST_SYSTEM_CONFIG]"
+    WORKTRUNK_TEST_BASH_INSTALLED: "0"
+    WORKTRUNK_TEST_CLAUDE_INSTALLED: "0"
+    WORKTRUNK_TEST_CODEX_INSTALLED: "0"
+    WORKTRUNK_TEST_DELAYED_STREAM_MS: "-1"
+    WORKTRUNK_TEST_EPOCH: "1735776000"
+    WORKTRUNK_TEST_FISH_INSTALLED: "0"
+    WORKTRUNK_TEST_GEMINI_INSTALLED: "0"
+    WORKTRUNK_TEST_NUSHELL_ENV: "0"
+    WORKTRUNK_TEST_OPENCODE_INSTALLED: "0"
+    WORKTRUNK_TEST_POWERSHELL_ENV: "0"
+    WORKTRUNK_TEST_POWERSHELL_INSTALLED: "0"
+    WORKTRUNK_TEST_SKIP_URL_HEALTH_CHECK: "1"
+    WORKTRUNK_TEST_ZSH_INSTALLED: "0"
+    XDG_CONFIG_HOME: "[TEST_CONFIG_HOME]"
+---
+success: true
+exit_code: 0
+----- stdout -----
+
+----- stderr -----
+✓ Created worktree for dep-no-cd @ _REPO_.dep-no-cd