diff --git a/docs/content/faq.md b/docs/content/faq.md
index f58050f1e1..b0e8845a7b 100644
--- a/docs/content/faq.md
+++ b/docs/content/faq.md
@@ -195,8 +195,8 @@ Use `-D` to force-delete branches with unmerged changes. Use `--no-delete-branch
 
 - `wt remove` — besides the target worktree, two cleanup mechanisms run. The removed worktree's own `git fsmonitor--daemon` (git's per-worktree filesystem watcher under `core.fsmonitor=true`, which would leak once its worktree is gone) is sent `git fsmonitor--daemon stop`, then force-terminated (`SIGTERM`, then `SIGKILL`) via the PID resolved from its IPC socket if it didn't exit. A background sweep then deletes `.git/wt/trash/` entries older than 24 hours (directories orphaned when a previous background removal was interrupted) and terminates fsmonitor daemons whose worktree no longer exists (orphans from `git worktree remove`, `rm -rf`, or a crashed `wt`)
 - `wt config state clear` — removes all worktrunk data from `.git/` (config keys, caches, markers, hints, variables, logs, stale trash)
-- `wt config shell install` — when migrating an integration to a new location, removes the worktrunk-managed file left at the old one: fish `conf.d/wt.fish` (now `functions/wt.fish`) and nushell wrappers stranded under `<config-dir>/vendor/autoload` (now `<data-dir>/vendor/autoload`). Recognition is the same as for uninstall below, so a file of the user's own sitting at that path is left in place
-- `wt config shell uninstall` — removes integration lines from bash/zsh/PowerShell rc files, and deletes worktrunk's wrapper and completion files (fish `functions/`, `conf.d/`, and `completions/`; nushell `vendor/autoload`). Files are recognized by worktrunk's own content markers, whatever binary name they were installed under; files without the markers are left alone. An rc file belongs to the user, so a line qualifies only where it runs the init command: one that merely mentions it, inside a comment, an `echo`, or an alias body, stays. Every line uninstall does take is printed, before removal and again after
+- `wt config shell install` — when migrating an integration to a new location, removes the file left at the old one: fish `conf.d/wt.fish` (now `functions/wt.fish`) and nushell wrappers stranded under `<config-dir>/vendor/autoload` (now `<data-dir>/vendor/autoload`). The old path is where worktrunk's own wrapper lived and is named after the command being installed, so it's taken back whole without reading it — a `conf.d/wt.fish` left in place would be sourced at startup and shadow the new wrapper anyway. Only that exact filename is touched, and each removal is printed
+- `wt config shell uninstall` — removes integration lines from bash/zsh/PowerShell rc files, and deletes worktrunk's wrapper and completion files (fish `functions/`, `conf.d/`, and `completions/`; nushell `vendor/autoload`). Uninstall takes no command name, so it lists those directories and recognizes files by worktrunk's own content markers, whatever binary name they were installed under; files without the markers are left alone. An rc file belongs to the user, so a line qualifies only where it runs the init command: one that merely mentions it, inside a comment, an `echo`, or an alias body, stays. Every line uninstall does take is printed, before removal and again after
 
 See [What files does Worktrunk create?](#what-files-does-worktrunk-create) for details.
 
diff --git a/plugins/worktrunk/skills/worktrunk/reference/faq.md b/plugins/worktrunk/skills/worktrunk/reference/faq.md
index fffae01e4f..63517fb487 100644
--- a/plugins/worktrunk/skills/worktrunk/reference/faq.md
+++ b/plugins/worktrunk/skills/worktrunk/reference/faq.md
@@ -190,8 +190,8 @@ Use `-D` to force-delete branches with unmerged changes. Use `--no-delete-branch
 
 - `wt remove` — besides the target worktree, two cleanup mechanisms run. The removed worktree's own `git fsmonitor--daemon` (git's per-worktree filesystem watcher under `core.fsmonitor=true`, which would leak once its worktree is gone) is sent `git fsmonitor--daemon stop`, then force-terminated (`SIGTERM`, then `SIGKILL`) via the PID resolved from its IPC socket if it didn't exit. A background sweep then deletes `.git/wt/trash/` entries older than 24 hours (directories orphaned when a previous background removal was interrupted) and terminates fsmonitor daemons whose worktree no longer exists (orphans from `git worktree remove`, `rm -rf`, or a crashed `wt`)
 - `wt config state clear` — removes all worktrunk data from `.git/` (config keys, caches, markers, hints, variables, logs, stale trash)
-- `wt config shell install` — when migrating an integration to a new location, removes the worktrunk-managed file left at the old one: fish `conf.d/wt.fish` (now `functions/wt.fish`) and nushell wrappers stranded under `<config-dir>/vendor/autoload` (now `<data-dir>/vendor/autoload`). Recognition is the same as for uninstall below, so a file of the user's own sitting at that path is left in place
-- `wt config shell uninstall` — removes integration lines from bash/zsh/PowerShell rc files, and deletes worktrunk's wrapper and completion files (fish `functions/`, `conf.d/`, and `completions/`; nushell `vendor/autoload`). Files are recognized by worktrunk's own content markers, whatever binary name they were installed under; files without the markers are left alone. An rc file belongs to the user, so a line qualifies only where it runs the init command: one that merely mentions it, inside a comment, an `echo`, or an alias body, stays. Every line uninstall does take is printed, before removal and again after
+- `wt config shell install` — when migrating an integration to a new location, removes the file left at the old one: fish `conf.d/wt.fish` (now `functions/wt.fish`) and nushell wrappers stranded under `<config-dir>/vendor/autoload` (now `<data-dir>/vendor/autoload`). The old path is where worktrunk's own wrapper lived and is named after the command being installed, so it's taken back whole without reading it — a `conf.d/wt.fish` left in place would be sourced at startup and shadow the new wrapper anyway. Only that exact filename is touched, and each removal is printed
+- `wt config shell uninstall` — removes integration lines from bash/zsh/PowerShell rc files, and deletes worktrunk's wrapper and completion files (fish `functions/`, `conf.d/`, and `completions/`; nushell `vendor/autoload`). Uninstall takes no command name, so it lists those directories and recognizes files by worktrunk's own content markers, whatever binary name they were installed under; files without the markers are left alone. An rc file belongs to the user, so a line qualifies only where it runs the init command: one that merely mentions it, inside a comment, an `echo`, or an alias body, stays. Every line uninstall does take is printed, before removal and again after
 
 See [What files does Worktrunk create?](#what-files-does-worktrunk-create) for details.
 
diff --git a/skills/worktrunk/reference/faq.md b/skills/worktrunk/reference/faq.md
index fffae01e4f..63517fb487 100644
--- a/skills/worktrunk/reference/faq.md
+++ b/skills/worktrunk/reference/faq.md
@@ -190,8 +190,8 @@ Use `-D` to force-delete branches with unmerged changes. Use `--no-delete-branch
 
 - `wt remove` — besides the target worktree, two cleanup mechanisms run. The removed worktree's own `git fsmonitor--daemon` (git's per-worktree filesystem watcher under `core.fsmonitor=true`, which would leak once its worktree is gone) is sent `git fsmonitor--daemon stop`, then force-terminated (`SIGTERM`, then `SIGKILL`) via the PID resolved from its IPC socket if it didn't exit. A background sweep then deletes `.git/wt/trash/` entries older than 24 hours (directories orphaned when a previous background removal was interrupted) and terminates fsmonitor daemons whose worktree no longer exists (orphans from `git worktree remove`, `rm -rf`, or a crashed `wt`)
 - `wt config state clear` — removes all worktrunk data from `.git/` (config keys, caches, markers, hints, variables, logs, stale trash)
-- `wt config shell install` — when migrating an integration to a new location, removes the worktrunk-managed file left at the old one: fish `conf.d/wt.fish` (now `functions/wt.fish`) and nushell wrappers stranded under `<config-dir>/vendor/autoload` (now `<data-dir>/vendor/autoload`). Recognition is the same as for uninstall below, so a file of the user's own sitting at that path is left in place
-- `wt config shell uninstall` — removes integration lines from bash/zsh/PowerShell rc files, and deletes worktrunk's wrapper and completion files (fish `functions/`, `conf.d/`, and `completions/`; nushell `vendor/autoload`). Files are recognized by worktrunk's own content markers, whatever binary name they were installed under; files without the markers are left alone. An rc file belongs to the user, so a line qualifies only where it runs the init command: one that merely mentions it, inside a comment, an `echo`, or an alias body, stays. Every line uninstall does take is printed, before removal and again after
+- `wt config shell install` — when migrating an integration to a new location, removes the file left at the old one: fish `conf.d/wt.fish` (now `functions/wt.fish`) and nushell wrappers stranded under `<config-dir>/vendor/autoload` (now `<data-dir>/vendor/autoload`). The old path is where worktrunk's own wrapper lived and is named after the command being installed, so it's taken back whole without reading it — a `conf.d/wt.fish` left in place would be sourced at startup and shadow the new wrapper anyway. Only that exact filename is touched, and each removal is printed
+- `wt config shell uninstall` — removes integration lines from bash/zsh/PowerShell rc files, and deletes worktrunk's wrapper and completion files (fish `functions/`, `conf.d/`, and `completions/`; nushell `vendor/autoload`). Uninstall takes no command name, so it lists those directories and recognizes files by worktrunk's own content markers, whatever binary name they were installed under; files without the markers are left alone. An rc file belongs to the user, so a line qualifies only where it runs the init command: one that merely mentions it, inside a comment, an `echo`, or an alias body, stays. Every line uninstall does take is printed, before removal and again after
 
 See [What files does Worktrunk create?](#what-files-does-worktrunk-create) for details.
 
diff --git a/src/commands/configure_shell.rs b/src/commands/configure_shell.rs
index 366215fab2..649d7aebcf 100644
--- a/src/commands/configure_shell.rs
+++ b/src/commands/configure_shell.rs
@@ -132,9 +132,15 @@ const WRAPPER_MARKER: &str = "worktrunk shell integration for";
 /// The header every fish completion file worktrunk has shipped opens with.
 const COMPLETION_MARKER: &str = "# worktrunk completions for";
 
-/// Whether a whole file is one worktrunk generated, and so is worktrunk's to
-/// delete — by `uninstall`, and by the install-time cleanup of the legacy fish
-/// `conf.d` wrapper.
+/// Whether a whole file is one worktrunk generated, and so is `uninstall`'s to
+/// delete.
+///
+/// This is the one place ownership is read out of a file's contents, because
+/// it's the one place worktrunk doesn't know the name. `uninstall` takes no
+/// `--cmd`, so it lists the shell-owned directories and has to tell worktrunk's
+/// `{cmd}.fish` from the user's own files sitting beside it. Wherever the
+/// command name *is* known — install, and the legacy-location cleanups that
+/// accompany it — the path names the file worktrunk owns and nothing reads it.
 ///
 /// The answer is independent of the binary name embedded in the file, so a
 /// wrapper installed as `wt.fish`, `git-wt.fish`, or `git-wt.nu` is recognized
@@ -145,10 +151,10 @@ const COMPLETION_MARKER: &str = "# worktrunk completions for";
 /// (per the rc-file line detector, keeping one definition of "an integration
 /// line").
 ///
-/// Both callers walk directories the user owns, so the question is asked of
-/// every line rather than of the file as a blob. A user's own `wt.fish` that
-/// runs `wt config shell init` amid other code — or merely mentions it in a
-/// comment — survives; a whole-file substring test would delete it.
+/// The directories walked are the user's, so the question is asked of every
+/// line rather than of the file as a blob. A user's own `wt.fish` that runs
+/// `wt config shell init` amid other code — or merely mentions it in a comment
+/// — survives; a whole-file substring test would delete it.
 fn is_worktrunk_managed_content(content: &str) -> bool {
     if content.contains(WRAPPER_MARKER) {
         return true;
@@ -160,21 +166,18 @@ fn is_worktrunk_managed_content(content: &str) -> bool {
             .all(shell::is_shell_integration_line_for_uninstall_any_cmd)
 }
 
-/// Check if a Nushell wrapper file is worktrunk-managed.
+/// Take back the fish wrapper's legacy `conf.d` location after installing to
+/// `functions/`.
 ///
-/// The Nushell wrapper is a complete autoload file (not a `source` line), so it
-/// carries no `config shell init` marker — the header comment is the whole
-/// signal that the file is ours to remove during stranded-file cleanup
-/// (issue #2878).
-fn is_worktrunk_managed_nushell(content: &str) -> bool {
-    content.contains(&format!("{WRAPPER_MARKER} nushell"))
-}
-
-/// Clean up legacy fish conf.d file after installing to functions/
+/// Fish integration used to install to `~/.config/fish/conf.d/{cmd}.fish`,
+/// which loads before Homebrew's PATH setup in `config.fish` (issue #566);
+/// installs now write `functions/{cmd}.fish`, autoloaded on first use.
 ///
-/// Previously, fish shell integration was installed to `~/.config/fish/conf.d/{cmd}.fish`.
-/// This caused issues with Homebrew PATH setup (see issue #566). We now install to
-/// `functions/{cmd}.fish` instead. This function removes the legacy file if it exists.
+/// The path names the command being installed, so it's worktrunk's and the file
+/// goes whole — the contents are never read. Leaving it would also break the
+/// install it accompanies: `conf.d` is sourced at startup, so a `function
+/// {cmd}` defined there is already loaded by the time fish would autoload
+/// `functions/{cmd}.fish`, and the stale wrapper wins every time.
 ///
 /// Returns the paths of files that were cleaned up, each paired with `Shell::Fish`.
 fn cleanup_legacy_fish_conf_d(configured: &[ConfigureResult], cmd: &str) -> Vec<(Shell, PathBuf)> {
@@ -198,16 +201,6 @@ fn cleanup_legacy_fish_conf_d(configured: &[ConfigureResult], cmd: &str) -> Vec<
         return cleaned;
     }
 
-    // Only remove if the file contains worktrunk integration markers
-    // to avoid deleting user's custom wt.fish that isn't from worktrunk
-    let Ok(content) = fs::read_to_string(&legacy_path) else {
-        return cleaned;
-    };
-
-    if !is_worktrunk_managed_content(&content) {
-        return cleaned;
-    }
-
     match fs::remove_file(&legacy_path) {
         Ok(()) => {
             cleaned.push((Shell::Fish, legacy_path));
@@ -231,9 +224,13 @@ fn cleanup_legacy_fish_conf_d(configured: &[ConfigureResult], cmd: &str) -> Vec<
 ///
 /// Older worktrunk installed the wrapper under `<config-dir>/vendor/autoload`,
 /// which Nushell never autoloads (issue #2878). After installing to the correct
-/// vendor-autoload dir (`<data-dir>/vendor/autoload`), this removes any
-/// worktrunk-managed wrapper left at the other candidate paths so a stale,
-/// never-loaded copy isn't left behind.
+/// vendor-autoload dir (`<data-dir>/vendor/autoload`), this removes the wrapper
+/// left at the other candidate paths so a stale, never-loaded copy isn't left
+/// behind.
+///
+/// Every path considered is one worktrunk itself computes for this command name
+/// (`config_paths`), so — as with the fish `conf.d` cleanup — the path settles
+/// ownership and the file is removed whole, unread.
 ///
 /// Returns the paths removed, each paired with `Shell::Nushell`.
 fn cleanup_stranded_nushell(configured: &[ConfigureResult], cmd: &str) -> Vec<(Shell, PathBuf)> {
@@ -254,14 +251,6 @@ fn cleanup_stranded_nushell(configured: &[ConfigureResult], cmd: &str) -> Vec<(S
         if &path == canonical || !path.exists() {
             continue;
         }
-        // Only remove files that are clearly worktrunk's, to avoid deleting a
-        // user's own `wt.nu`.
-        let Ok(content) = fs::read_to_string(&path) else {
-            continue;
-        };
-        if !is_worktrunk_managed_nushell(&content) {
-            continue;
-        }
         match fs::remove_file(&path) {
             Ok(()) => cleaned.push((Shell::Nushell, path)),
             Err(e) => {
@@ -1633,12 +1622,12 @@ mod tests {
             assert!(is_worktrunk_managed_content(content), "{content}");
         }
 
-        // Not ours: both callers walk directories the user owns, so a file that
-        // only mentions the command must survive — as must a user's own file
-        // that runs the init line amid other code, which a per-line any-match
-        // would delete whole. The second and third also carry the init command
-        // and a `| source` somewhere, which is all a whole-file substring test
-        // asks before deleting.
+        // Not ours: the uninstall scan walks directories the user owns and has
+        // only the contents to go on, so a file that merely mentions the command
+        // must survive — as must a user's own file that runs the init line amid
+        // other code, which a per-line any-match would delete whole. The second
+        // and third also carry the init command and a `| source` somewhere,
+        // which is all a whole-file substring test asks before deleting.
         for content in [
             "function notes\n    echo run wt config shell init fish to set up\nend\n",
             "# reminder: wt config shell init fish\nfunction helpers\n    cat ~/.aliases | source\nend\n",
diff --git a/tests/integration_tests/configure_shell.rs b/tests/integration_tests/configure_shell.rs
index 30e9f3bcd6..f0aa51c55c 100644
--- a/tests/integration_tests/configure_shell.rs
+++ b/tests/integration_tests/configure_shell.rs
@@ -408,20 +408,23 @@ fn test_configure_shell_fish_legacy_conf_d_cleanup(repo: TestRepo, temp_home: Te
     );
 }
 
-/// Installing fish integration leaves a user's own `conf.d/wt.fish` alone.
+/// Installing fish integration reclaims `conf.d/{cmd}.fish` whatever it holds.
 ///
-/// The legacy cleanup deletes a whole file the user never asked it to touch, so
-/// it has to recognize worktrunk's own wrapper rather than any file that
-/// mentions the init command. This one names it in a comment and pipes
-/// something unrelated to `source` — both substrings a whole-file test would
-/// take as proof the file was worktrunk's.
+/// The path names the command being installed, so it's worktrunk's; the file's
+/// contents don't enter into it. Leaving this one would break the install
+/// besides — `conf.d` is sourced at startup, so a `function wt` defined there
+/// is already loaded when fish would otherwise autoload `functions/wt.fish`.
 #[rstest]
-fn test_configure_shell_fish_preserves_user_conf_d_file(repo: TestRepo, temp_home: TempDir) {
+fn test_configure_shell_fish_reclaims_conf_d_path(repo: TestRepo, temp_home: TempDir) {
     let conf_d = temp_home.path().join(".config/fish/conf.d");
     fs::create_dir_all(&conf_d).unwrap();
-    let user_file = conf_d.join("wt.fish");
-    let user_content = "# reminder: set up with wt config shell init fish\nfunction wt_helpers\n    cat ~/.aliases | source\nend\n";
-    fs::write(&user_file, user_content).unwrap();
+    let stale = conf_d.join("wt.fish");
+    // No worktrunk header, and nothing a content test would recognize.
+    fs::write(&stale, "function wt\n    command wt-old $argv\nend\n").unwrap();
+    // A neighbour under another name is untouched: only `{cmd}.fish` is ours.
+    let neighbour = conf_d.join("aliases.fish");
+    let neighbour_content = "# reminder: wt config shell init fish\nalias ll 'ls -l'\n";
+    fs::write(&neighbour, neighbour_content).unwrap();
 
     let mut cmd = wt_command();
     repo.configure_wt_cmd(&mut cmd);
@@ -437,16 +440,22 @@ fn test_configure_shell_fish_preserves_user_conf_d_file(repo: TestRepo, temp_hom
             .path()
             .join(".config/fish/functions/wt.fish")
             .exists(),
-        "install should still write functions/wt.fish"
+        "install should write functions/wt.fish"
     );
     assert!(
-        user_file.exists(),
-        "install deleted the user's own conf.d/wt.fish"
+        !stale.exists(),
+        "install should reclaim conf.d/wt.fish: {stale:?}"
     );
     assert_eq!(
-        fs::read_to_string(&user_file).unwrap(),
-        user_content,
-        "user's own conf.d/wt.fish must survive install untouched"
+        fs::read_to_string(&neighbour).unwrap(),
+        neighbour_content,
+        "a conf.d file under another name is not worktrunk's"
+    );
+    // The removal is reported, not silent.
+    let stderr = String::from_utf8_lossy(&output.stderr);
+    assert!(
+        stderr.contains("deprecated"),
+        "install should report the conf.d cleanup:\n{stderr}"
     );
 }
 
@@ -2774,21 +2783,23 @@ fn test_nushell_install_cleans_stranded_legacy(repo: TestRepo, temp_home: TempDi
     );
 }
 
-/// Data safety: install must NOT delete a `wt.nu` at a legacy location that
-/// isn't worktrunk-managed (no worktrunk header) — it could be the user's own
-/// file. Only files carrying the worktrunk header are cleaned up (issue #2878).
+/// The stranded-file cleanup is scoped by path, so it reclaims `{cmd}.nu` at a
+/// legacy autoload dir whatever the file holds — and touches nothing else in
+/// that directory (issue #2878).
 #[rstest]
-fn test_nushell_install_keeps_unmanaged_legacy_file(repo: TestRepo, temp_home: TempDir) {
+fn test_nushell_install_reclaims_only_the_command_name(repo: TestRepo, temp_home: TempDir) {
     let home = canonical_temp_home(&temp_home);
     let autoload = home.join(".local/share/nushell/vendor/autoload");
 
-    // A user-authored wt.nu at the legacy config-dir location — no worktrunk
-    // header, so it must be left untouched.
     let legacy_dir = home.join(".config/nushell/vendor/autoload");
     fs::create_dir_all(&legacy_dir).unwrap();
+    // No worktrunk header: the path is what makes it worktrunk's.
     let legacy = legacy_dir.join("wt.nu");
-    let user_content = "# my own wt helper\ndef wt [] { echo hi }\n";
-    fs::write(&legacy, user_content).unwrap();
+    fs::write(&legacy, "def wt [] { echo hi }\n").unwrap();
+    // A neighbour under another name stays put.
+    let neighbour = legacy_dir.join("helpers.nu");
+    let neighbour_content = "def hi [] { echo hi }\n";
+    fs::write(&neighbour, neighbour_content).unwrap();
 
     let mut cmd = wt_command();
     repo.configure_wt_cmd(&mut cmd);
@@ -2805,16 +2816,15 @@ fn test_nushell_install_keeps_unmanaged_legacy_file(repo: TestRepo, temp_home: T
         String::from_utf8_lossy(&output.stderr)
     );
 
-    // Canonical wrapper written, user's legacy file preserved verbatim.
     assert!(autoload.join("wt.nu").exists(), "canonical wrapper missing");
     assert!(
-        legacy.exists(),
-        "unmanaged legacy wt.nu must be preserved: {legacy:?}"
+        !legacy.exists(),
+        "install should reclaim the legacy wt.nu: {legacy:?}"
     );
     assert_eq!(
-        fs::read_to_string(&legacy).unwrap(),
-        user_content,
-        "unmanaged legacy file must be left unchanged"
+        fs::read_to_string(&neighbour).unwrap(),
+        neighbour_content,
+        "a legacy-dir file under another name is not worktrunk's"
     );
 }