add --keep-untracked option to uv sync, default in uv add/run

crates/uv/src/cli.rs

@@ -1544,6 +1544,11 @@ pub(crate) struct SyncArgs {
     #[arg(long, overrides_with("dev"))]
     pub(crate) no_dev: bool,
 
+    /// Keeps installations no tracked as dependencies.
+    /// Without this flag any extraneous installations will be removed.
+    #[arg(long)]
+    pub(crate) keep_untracked: bool,
+
     #[command(flatten)]
     pub(crate) installer: InstallerArgs,
 

crates/uv/src/commands/mod.rs

@@ -40,7 +40,7 @@ use crate::printer::Printer;
 mod cache_clean;
 mod cache_dir;
 mod cache_prune;
-mod pip;
+pub(crate) mod pip;
 mod project;
 pub(crate) mod reporters;
 mod tool;

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

@@ -12,6 +12,7 @@ use uv_configuration::{Concurrency, ExtrasSpecification, PreviewMode, SetupPyStr
 use uv_distribution::{DistributionDatabase, ProjectWorkspace};
 use uv_warnings::warn_user;
 
+use crate::commands::pip::operations::Modifications;
 use crate::commands::pip::resolution_environment;
 use crate::commands::reporters::ResolverReporter;
 use crate::commands::{project, ExitStatus};
@@ -172,6 +173,7 @@ pub(crate) async fn add(
         &lock,
         extras,
         dev,
+        Modifications::Sufficient,
         &settings.reinstall,
         &settings.index_locations,
         &settings.index_strategy,

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

@@ -8,6 +8,7 @@ use uv_distribution::pyproject_mut::PyProjectTomlMut;
 use uv_distribution::ProjectWorkspace;
 use uv_warnings::warn_user;
 
+use crate::commands::pip::operations::Modifications;
 use crate::commands::{project, ExitStatus};
 use crate::printer::Printer;
 use crate::settings::{InstallerSettings, ResolverSettings};
@@ -121,6 +122,7 @@ pub(crate) async fn remove(
         &lock,
         extras,
         dev,
+        Modifications::Exact,
         &settings.reinstall,
         &settings.index_locations,
         &settings.index_strategy,

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

@@ -15,6 +15,7 @@ use uv_requirements::RequirementsSource;
 use uv_toolchain::{PythonEnvironment, SystemPython, Toolchain, ToolchainRequest};
 use uv_warnings::warn_user;
 
+use crate::commands::pip::operations::Modifications;
 use crate::commands::{project, ExitStatus};
 use crate::printer::Printer;
 use crate::settings::ResolverInstallerSettings;
@@ -91,6 +92,7 @@ pub(crate) async fn run(
             &lock,
             extras,
             dev,
+            Modifications::Sufficient,
             &settings.reinstall,
             &settings.index_locations,
             &settings.index_strategy,

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

@@ -31,6 +31,7 @@ use crate::settings::InstallerSettings;
 pub(crate) async fn sync(
     extras: ExtrasSpecification,
     dev: bool,
+    modifications: Modifications,
     python: Option<String>,
     settings: InstallerSettings,
     preview: PreviewMode,
@@ -65,6 +66,7 @@ pub(crate) async fn sync(
         &lock,
         extras,
         dev,
+        modifications,
         &settings.reinstall,
         &settings.index_locations,
         &settings.index_strategy,
@@ -94,6 +96,7 @@ pub(super) async fn do_sync(
     lock: &Lock,
     extras: ExtrasSpecification,
     dev: bool,
+    modifications: Modifications,
     reinstall: &Reinstall,
     index_locations: &IndexLocations,
     index_strategy: &IndexStrategy,
@@ -188,7 +191,7 @@ pub(super) async fn do_sync(
     pip::operations::install(
         &resolution,
         site_packages,
-        Modifications::Exact,
+        modifications,
         reinstall,
         build_options,
         *link_mode,

crates/uv/src/main.rs

@@ -646,6 +646,7 @@ async fn run() -> Result<ExitStatus> {
             commands::sync(
                 args.extras,
                 args.dev,
+                args.modifications,
                 args.python,
                 args.settings,
                 globals.preview,

crates/uv/src/settings.rs

@@ -31,6 +31,7 @@ use crate::cli::{
     RunArgs, SyncArgs, ToolRunArgs, ToolchainFindArgs, ToolchainInstallArgs, ToolchainListArgs,
     VenvArgs,
 };
+use crate::commands::pip::operations::Modifications;
 use crate::commands::ListFormat;
 
 /// The resolved global settings to use for any invocation of the CLI.
@@ -297,6 +298,7 @@ impl ToolchainFindSettings {
 pub(crate) struct SyncSettings {
     pub(crate) extras: ExtrasSpecification,
     pub(crate) dev: bool,
+    pub(crate) modifications: Modifications,
     pub(crate) python: Option<String>,
     pub(crate) refresh: Refresh,
     pub(crate) settings: InstallerSettings,
@@ -312,18 +314,26 @@ impl SyncSettings {
             no_all_extras,
             dev,
             no_dev,
+            keep_untracked,
             installer,
             build,
             refresh,
             python,
         } = args;
 
+        let modifications = if keep_untracked {
+            Modifications::Sufficient
+        } else {
+            Modifications::Exact
+        };
+
         Self {
             extras: ExtrasSpecification::from_args(
                 flag(all_extras, no_all_extras).unwrap_or_default(),
                 extra.unwrap_or_default(),
             ),
             dev: flag(dev, no_dev).unwrap_or(true),
+            modifications,
             python,
             refresh: Refresh::from(refresh),
             settings: InstallerSettings::combine(installer_options(installer, build), filesystem),