fix: allow envars to be overriden in active environments

env.go

@@ -748,6 +748,7 @@ func (e *Env) Exec(l *ui.UI, pkg *manifest.Package, binary string, args []string
 		return errors.WithStack(err)
 	}
 	ops := e.allEnvarOpsForPackages(runtimeDeps, pkg, installed...)
+	ops = append(ops, e.systemEnvOverrideOps(ops)...)
 	packageHermitBin, err := e.getPackageRuntimeEnvops(pkg)
 	if err != nil {
 		return errors.WithStack(err)
@@ -777,6 +778,23 @@ func (e *Env) Exec(l *ui.UI, pkg *manifest.Package, binary string, args []string
 	return errors.Errorf("%s: could not find binary %q", pkg, binary)
 }
 
+// systemEnvOverrideOps returns environment variables defined in the system environment that were previously overriden by Hermit
+func (e *Env) systemEnvOverrideOps(ops envars.Ops) envars.Ops {
+	if activeEnv, ok := os.LookupEnv("HERMIT_ENV"); !ok || activeEnv != e.envDir {
+		return envars.Ops{}
+	}
+
+	var overrides envars.Ops
+	for _, op := range ops {
+		envar := op.Envar()
+		if v, ok := os.LookupEnv(envar); ok {
+			overrides = append(overrides, &envars.Force{Name: envar, Value: v})
+		}
+	}
+
+	return overrides
+}
+
 func (e *Env) getPackageRuntimeEnvops(pkg *manifest.Package) (envars.Op, error) {
 	// If the package contains a Hermit env, add that to the PATH for runtime dependencies
 	pkgEnv, err := OpenEnv(pkg.Root, e.state, e.packageSource, nil, e.httpClient, e.scriptSums)

integration/integration_test.go

@@ -265,6 +265,16 @@ func TestIntegration(t *testing.T) {
 			assert test "$(testbin1.sh)" = "FOO=runtimefoo"
 			assert test "$(testbin2.sh)" = "BAR=hermitbar"
 			`},
+		{name: "SystemEnvOverridesAlreadyAcitvatedHermitEnv",
+			preparations: prep{fixture("testenv4"), activate(".")},
+			script: `
+			hermit install testbin1
+			hermit install testbin2
+			export FOO=systemfoo
+			assert test "$(testbin1.sh)" = "FOO=systemfoo"
+			export BAR=systembar
+			assert test "$(testbin2.sh)" = "BAR=systembar"
+			`},
 	}
 
 	checkForShells(t)