Fix devbox update <pkg> installing all packages instead of just the target

When running `devbox update <pkg>`, packagesToInstallInStore() was
unconditionally adding every package to the install list in update mode.
This caused all packages to be re-installed with --refresh, not just the
ones the user requested.

Track which packages are being updated via a field on the Devbox struct
and only force-install those in packagesToInstallInStore(). Other packages
still go through the normal store-path check.

Fixes #2653

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: mikeland73

internal/devbox/devbox.go

@@ -68,6 +68,10 @@ type Devbox struct {
 
 	// This is needed because of the --quiet flag.
 	stderr io.Writer
+
+	// packagesBeingUpdated tracks which packages are being updated so that
+	// installNixPackagesToStore only refreshes those, not all packages.
+	packagesBeingUpdated []*devpkg.Package
 }
 
 var legacyPackagesWarningHasBeenShown = false

internal/devbox/packages.go

@@ -637,7 +637,7 @@ func (d *Devbox) packagesToInstallInStore(ctx context.Context, mode installMode)
 	packagesToInstall := []*devpkg.Package{}
 	storePathsForPackage := map[*devpkg.Package][]string{}
 	for _, pkg := range packages {
-		if mode == update {
+		if mode == update && d.isBeingUpdated(pkg) {
 			packagesToInstall = append(packagesToInstall, pkg)
 			continue
 		}
@@ -666,6 +666,15 @@ func (d *Devbox) packagesToInstallInStore(ctx context.Context, mode installMode)
 	return lo.Uniq(packagesToInstall), nil
 }
 
+func (d *Devbox) isBeingUpdated(pkg *devpkg.Package) bool {
+	for _, u := range d.packagesBeingUpdated {
+		if u.Raw == pkg.Raw {
+			return true
+		}
+	}
+	return false
+}
+
 // moveAllowInsecureFromLockfile will modernize a Devbox project by moving the allow_insecure: boolean
 // setting from the devbox.lock file to the corresponding package in devbox.json.
 //

internal/devbox/update.go

@@ -80,6 +80,8 @@ func (d *Devbox) Update(ctx context.Context, opts devopt.UpdateOpts) error {
 		}
 	}
 
+	d.packagesBeingUpdated = inputs
+
 	mode := update
 	if opts.NoInstall {
 		mode = noInstall