Add some missing reinstall-refresh calls (#5497)

## Summary

Turns out I missed a few of these.

crates/uv/src/lib.rs

@@ -179,8 +179,9 @@ async fn run(cli: Cli) -> Result<ExitStatus> {
                 .expect("failed to initialize global rayon pool");
 
             // Initialize the cache.
-
-            let cache = cache.init()?.with_refresh(args.refresh);
+            let cache = cache
+                .init()?
+                .with_refresh(args.settings.reinstall.clone().to_refresh(args.refresh));
 
             let requirements = args
                 .src_file
@@ -626,7 +627,9 @@ async fn run(cli: Cli) -> Result<ExitStatus> {
             show_settings!(args);
 
             // Initialize the cache.
-            let cache = cache.init()?.with_refresh(args.refresh);
+            let cache = cache
+                .init()?
+                .with_refresh(args.settings.reinstall.clone().to_refresh(args.refresh));
 
             let requirements = args
                 .with
@@ -666,7 +669,9 @@ async fn run(cli: Cli) -> Result<ExitStatus> {
             show_settings!(args);
 
             // Initialize the cache.
-            let cache = cache.init()?.with_refresh(args.refresh);
+            let cache = cache
+                .init()?
+                .with_refresh(args.settings.reinstall.clone().to_refresh(args.refresh));
 
             let requirements = args
                 .with

crates/uv/tests/tool_install.rs

@@ -740,6 +740,7 @@ fn tool_install_already_installed() {
     ----- stderr -----
     warning: `uv tool install` is experimental and may change without warning
     Resolved [N] packages in [TIME]
+    Prepared [N] packages in [TIME]
     Uninstalled [N] packages in [TIME]
     Installed [N] packages in [TIME]
      - black==24.3.0
@@ -773,6 +774,7 @@ fn tool_install_already_installed() {
     ----- stderr -----
     warning: `uv tool install` is experimental and may change without warning
     Resolved [N] packages in [TIME]
+    Prepared [N] packages in [TIME]
     Uninstalled [N] packages in [TIME]
     Installed [N] packages in [TIME]
      - black==24.3.0
@@ -796,6 +798,7 @@ fn tool_install_already_installed() {
     ----- stderr -----
     warning: `uv tool install` is experimental and may change without warning
     Resolved [N] packages in [TIME]
+    Prepared [N] packages in [TIME]
     Uninstalled [N] packages in [TIME]
     Installed [N] packages in [TIME]
      - click==8.1.7
@@ -869,6 +872,7 @@ fn tool_install_entry_point_exists() {
     ----- stderr -----
     warning: `uv tool install` is experimental and may change without warning
     Resolved [N] packages in [TIME]
+    Prepared [N] packages in [TIME]
     Installed [N] packages in [TIME]
      + black==24.3.0
      + click==8.1.7
@@ -995,6 +999,7 @@ fn tool_install_entry_point_exists() {
     ----- stderr -----
     warning: `uv tool install` is experimental and may change without warning
     Resolved [N] packages in [TIME]
+    Prepared [N] packages in [TIME]
     Uninstalled [N] packages in [TIME]
     Installed [N] packages in [TIME]
      - black==24.3.0