Ensure all roots of an installed environment are marked explicit in db (#24277)

lib/spack/spack/environment.py

@@ -1574,6 +1574,13 @@ def install_specs(self, specs=None, args=None, **install_args):
         specs_to_install = [s for s in specs_to_install
                             if s not in self.roots() or s in uninstalled_roots]
 
+        # ensure specs already installed are marked explicit
+        all_specs = specs or [cs for _, cs in self.concretized_specs()]
+        specs_installed = [s for s in all_specs if s.package.installed]
+        with spack.store.db.write_transaction():  # do all in one transaction
+            for spec in specs_installed:
+                spack.store.db.update_explicit(spec, True)
+
         if not specs_to_install:
             tty.msg('All of the packages are already installed')
             return

lib/spack/spack/test/cmd/env.py

@@ -179,6 +179,27 @@ def test_env_install_single_spec(install_mockery, mock_fetch):
     assert e.specs_by_hash[e.concretized_order[0]].name == 'cmake-client'
 
 
+def test_env_roots_marked_explicit(install_mockery, mock_fetch):
+    install = SpackCommand('install')
+    install('dependent-install')
+
+    # Check one explicit, one implicit install
+    dependent = spack.store.db.query(explicit=True)
+    dependency = spack.store.db.query(explicit=False)
+    assert len(dependent) == 1
+    assert len(dependency) == 1
+
+    env('create', 'test')
+    with ev.read('test') as e:
+        # make implicit install a root of the env
+        e.add(dependency[0].name)
+        e.concretize()
+        e.install_all()
+
+    explicit = spack.store.db.query(explicit=True)
+    assert len(explicit) == 2
+
+
 def test_env_modifications_error_on_activate(
         install_mockery, mock_fetch, monkeypatch, capfd):
     env('create', 'test')