Allow sync and update environment methods to take modifications (#11346)

## Summary

I have a use-case for an inexact sync here, so putting this up
separately.

crates/uv/src/commands/project/environment.rs

@@ -11,6 +11,7 @@ use uv_python::{Interpreter, PythonEnvironment};
 use uv_resolver::Installable;
 
 use crate::commands::pip::loggers::{InstallLogger, ResolveLogger};
+use crate::commands::pip::operations::Modifications;
 use crate::commands::project::install_target::InstallTarget;
 use crate::commands::project::{
     resolve_environment, sync_environment, EnvironmentSpecification, PlatformState, ProjectError,
@@ -193,6 +194,7 @@ impl CachedEnvironment {
         sync_environment(
             venv,
             &resolution,
+            Modifications::Exact,
             settings.as_ref().into(),
             state,
             install,

crates/uv/src/commands/project/mod.rs

@@ -1438,6 +1438,7 @@ pub(crate) async fn resolve_environment(
 pub(crate) async fn sync_environment(
     venv: PythonEnvironment,
     resolution: &Resolution,
+    modifications: Modifications,
     settings: InstallerSettingsRef<'_>,
     state: &PlatformState,
     logger: Box<dyn InstallLogger>,
@@ -1546,7 +1547,7 @@ pub(crate) async fn sync_environment(
     pip::operations::install(
         resolution,
         site_packages,
-        Modifications::Exact,
+        modifications,
         reinstall,
         build_options,
         link_mode,
@@ -1594,6 +1595,7 @@ impl EnvironmentUpdate {
 pub(crate) async fn update_environment(
     venv: PythonEnvironment,
     spec: RequirementsSpecification,
+    modifications: Modifications,
     settings: &ResolverInstallerSettings,
     state: &SharedState,
     resolve: Box<dyn ResolveLogger>,
@@ -1794,7 +1796,7 @@ pub(crate) async fn update_environment(
     let changelog = pip::operations::install(
         &resolution,
         site_packages,
-        Modifications::Exact,
+        modifications,
         reinstall,
         build_options,
         *link_mode,

crates/uv/src/commands/tool/install.rs

@@ -24,6 +24,7 @@ use uv_warnings::warn_user;
 
 use crate::commands::pip::loggers::{DefaultInstallLogger, DefaultResolveLogger};
 
+use crate::commands::pip::operations::Modifications;
 use crate::commands::project::{
     resolve_environment, resolve_names, sync_environment, update_environment,
     EnvironmentSpecification, PlatformState, ProjectError,
@@ -422,6 +423,7 @@ pub(crate) async fn install(
         let environment = match update_environment(
             environment,
             spec,
+            Modifications::Exact,
             &settings,
             &state,
             Box::new(DefaultResolveLogger),
@@ -551,6 +553,7 @@ pub(crate) async fn install(
         match sync_environment(
             environment,
             &resolution.into(),
+            Modifications::Exact,
             settings.as_ref().into(),
             &state,
             Box::new(DefaultInstallLogger),

crates/uv/src/commands/tool/upgrade.rs

@@ -22,6 +22,7 @@ use uv_tool::InstalledTools;
 use crate::commands::pip::loggers::{
     DefaultInstallLogger, SummaryResolveLogger, UpgradeInstallLogger,
 };
+use crate::commands::pip::operations::Modifications;
 use crate::commands::project::{
     resolve_environment, sync_environment, update_environment, EnvironmentUpdate, PlatformState,
 };
@@ -314,6 +315,7 @@ async fn upgrade_tool(
         let environment = sync_environment(
             environment,
             &resolution.into(),
+            Modifications::Exact,
             settings.as_ref().into(),
             &state,
             Box::new(DefaultInstallLogger),
@@ -339,6 +341,7 @@ async fn upgrade_tool(
         } = update_environment(
             environment,
             spec,
+            Modifications::Exact,
             &settings,
             &state,
             Box::new(SummaryResolveLogger),