[Fix #687] Improve project root detection with preferred build tool and VCS tiebreaker

When multiple build tool files exist in the directory hierarchy (e.g. a
source file named project.clj inside a deps.edn project), the most nested
match was always chosen, which could be incorrect.

Add `clojure-preferred-build-tool` defcustom for explicit user preference.
When unset, use `.git` presence as a tiebreaker before falling back to
most nested.

Author: bbatsov

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### New features
 
+* [#687](https://github.com/clojure-emacs/clojure-mode/issues/687): Add `clojure-preferred-build-tool` to control project root detection when multiple build tool files exist. When unset, prefer directories containing `.git` as a tiebreaker.
 * [#688](https://github.com/clojure-emacs/clojure-mode/issues/688): Add `clojure-discard-face` for `#_` reader discard forms, allowing them to be styled differently from comments. Inherits from `font-lock-comment-face` by default.
 * Add project root detection for ClojureCLR (`deps-clr.edn`).
 

clojure-mode.el

@@ -267,6 +267,22 @@ The prefixes are used to generate the correct namespace."
   :risky t
   :package-version '(clojure-mode . "5.7.0"))
 
+(defcustom clojure-preferred-build-tool nil
+  "Preferred build tool file to identify the project root.
+When multiple build tool files are found in the directory hierarchy,
+this setting controls which one takes precedence.
+
+When nil (the default), prefer directories that also contain a
+version-control marker (`.git').  If that doesn't break the tie,
+fall back to the most nested match.
+
+When set to a string (e.g., \"deps.edn\"), prefer the directory
+containing that specific file."
+  :type '(choice (const :tag "Auto-detect" nil)
+                 (string :tag "Build tool filename"))
+  :safe (lambda (value) (or (null value) (stringp value)))
+  :package-version '(clojure-mode . "5.22.0"))
+
 (defcustom clojure-refactor-map-prefix (kbd "C-c C-r")
   "Clojure refactor keymap prefix."
   :type 'string
@@ -2076,8 +2092,16 @@ Return nil if not inside a project."
                         (mapcar (lambda (fname)
                                   (locate-dominating-file dir-name fname))
                                 clojure-build-tool-files))))
-    (when (> (length choices) 0)
-      (car (sort choices #'file-in-directory-p)))))
+    (when choices
+      (if clojure-preferred-build-tool
+          ;; When a preferred build tool is set, look for it specifically.
+          (or (locate-dominating-file dir-name clojure-preferred-build-tool)
+              (car (sort choices #'file-in-directory-p)))
+        ;; Otherwise, prefer candidates that contain a .git directory.
+        (or (car (seq-filter (lambda (dir)
+                               (file-directory-p (expand-file-name ".git" dir)))
+                             (sort choices #'file-in-directory-p)))
+            (car choices))))))
 
 (defun clojure-project-relative-path (path)
   "Denormalize PATH by making it relative to the project root."

test/clojure-mode-util-test.el

@@ -47,7 +47,42 @@
           (write-region "{}" nil bb-edn)
           (make-directory bb-edn-src)
           (expect  (expand-file-name (clojure-project-dir bb-edn-src))
-                   :to-equal (file-name-as-directory temp-dir))))))
+                   :to-equal (file-name-as-directory temp-dir)))))
+
+    (it "preferred build tool selects matching directory"
+      (with-temp-dir temp-dir
+        (let* ((root (file-name-as-directory temp-dir))
+               (subdir (expand-file-name "src/project.clj" temp-dir))
+               (clojure-preferred-build-tool "deps.edn"))
+          (write-region "{}" nil (expand-file-name "deps.edn" temp-dir))
+          (make-directory (expand-file-name "src" temp-dir))
+          (write-region "" nil subdir)
+          (expect (expand-file-name
+                   (clojure-project-root-path (expand-file-name "src/" temp-dir)))
+                  :to-equal root))))
+
+    (it "VCS tiebreaker prefers directory with .git"
+      (with-temp-dir temp-dir
+        (let* ((root (file-name-as-directory temp-dir))
+               (clojure-preferred-build-tool nil))
+          (write-region "{}" nil (expand-file-name "deps.edn" temp-dir))
+          (make-directory (expand-file-name ".git" temp-dir))
+          (make-directory (expand-file-name "src" temp-dir))
+          (write-region "" nil (expand-file-name "src/project.clj" temp-dir))
+          (expect (expand-file-name
+                   (clojure-project-root-path (expand-file-name "src/" temp-dir)))
+                  :to-equal root))))
+
+    (it "no preference and no VCS falls back to most nested"
+      (with-temp-dir temp-dir
+        (let* ((subdir (file-name-as-directory (expand-file-name "src" temp-dir)))
+               (clojure-preferred-build-tool nil))
+          (write-region "{}" nil (expand-file-name "deps.edn" temp-dir))
+          (make-directory (expand-file-name "src" temp-dir))
+          (write-region "" nil (expand-file-name "src/project.clj" temp-dir))
+          (expect (expand-file-name
+                   (clojure-project-root-path (expand-file-name "src/" temp-dir)))
+                  :to-equal subdir)))))
 
   (describe "clojure-project-relative-path"
     (cl-letf (((symbol-function 'clojure-project-dir) (lambda () project-dir)))