diff --git a/src/snapshot/mod.rs b/src/snapshot/mod.rs
index 08cb6b31..47ef4794 100644
--- a/src/snapshot/mod.rs
+++ b/src/snapshot/mod.rs
@@ -1,8 +1,32 @@
 //! This module defines the instance snapshot subsystem of Rojo.
 //!
-//! It defines a way to define the instance tree of a project as a pure function
-//! of the filesystem by providing a lightweight instance 'snapshot' type, a
-//! method to generate minimal patches, and a method that applies those patches.
+//! Snapshots define a way to define the instance tree of a project as a pure
+//! function of the filesystem by providing a lightweight instance 'snapshot'
+//! type, a method to generate minimal patches, and a method that applies those
+//! patches.
+//!
+//! Changes in Rojo go through a pipeline of transformations once they hit the
+//! snapshot subsystem.
+//!
+//! 1. Instance snapshots are generated by Rojo's snapshot middleware,
+//!    representing a set of instances and their metadata. These will
+//!    usually contain data that hasn't actually changed, and how coarsely
+//!    the snapshots happen is defined outside this part of the code.
+//!
+//! 2. Input snapshots are turned into `PatchSet` objects by Rojo's diffing
+//!    algorithm via `compute_patch_set`. This operation doesn't mutate the
+//!    instance tree, so work at this point can be thrown away.
+//!
+//!    `PatchSet` prescribe what changes need to be applied to the current
+//!    tree to get the next tree. It isn't useful for describing those
+//!    changes after the fact, since Rojo needs to assign IDs to created
+//!    instances, which happens during patch application, not generation!
+//!
+//! 3. Patch sets are applied to the tree with `apply_patch_set`, which
+//!    mutates the relevant instances. `apply_patch_set` returns a new
+//!    object, `AppliedPatchSet`. Applied patch sets describe the transform
+//!    that was applied, and are suitable for cases where another tree needs
+//!    to be synchronized with Rojo's, like the Rojo Studio plugin.
 //!
 //! The aim with this approach is to reduce the number of bugs that arise from
 //! attempting to manually update instances in response to filesystem updates.
@@ -26,7 +50,7 @@ mod patch_compute;
 mod tree;
 
 pub use instance_snapshot::InstanceSnapshot;
-pub use metadata::*;
+pub use metadata::InstanceMetadata;
 pub use patch::*;
 pub use patch_apply::apply_patch_set;
 pub use patch_compute::compute_patch_set;
diff --git a/src/snapshot/patch.rs b/src/snapshot/patch.rs
index ca77df7c..7833a677 100644
--- a/src/snapshot/patch.rs
+++ b/src/snapshot/patch.rs
@@ -60,7 +60,7 @@ pub struct PatchUpdate {
 ///
 // TODO: Introduce machinery to detect conflicts, like keeping previous +
 // current values in all fields.
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Default)]
 pub struct AppliedPatchSet {
     pub removed: Vec<RbxId>,
     pub added: Vec<AppliedPatchAdd>,
diff --git a/src/snapshot/patch_apply.rs b/src/snapshot/patch_apply.rs
index 0d7c9b78..7463f3c6 100644
--- a/src/snapshot/patch_apply.rs
+++ b/src/snapshot/patch_apply.rs
@@ -13,7 +13,7 @@ pub fn apply_patch_set(tree: &mut RojoTree, patch_set: PatchSet) -> AppliedPatch
     let mut context = PatchApplyContext::default();
 
     for removed_id in patch_set.removed_instances {
-        tree.remove_instance(removed_id);
+        apply_remove_instance(&mut context, tree, removed_id);
     }
 
     for add_patch in patch_set.added_instances {
@@ -21,22 +21,21 @@ pub fn apply_patch_set(tree: &mut RojoTree, patch_set: PatchSet) -> AppliedPatch
     }
 
     for update_patch in patch_set.updated_instances {
-        apply_update_child(&context, tree, update_patch);
+        apply_update_child(&mut context, tree, update_patch);
     }
 
-    apply_deferred_properties(context, tree);
-
-    // TODO: Actually calculate patch set
-    AppliedPatchSet::new()
+    finalize_patch_application(context, tree)
 }
 
 #[derive(Default)]
 struct PatchApplyContext {
     snapshot_id_to_instance_id: HashMap<RbxId, RbxId>,
     properties_to_apply: HashMap<RbxId, HashMap<String, RbxValue>>,
+    applied_patch_set: AppliedPatchSet,
 }
 
-/// Apply properties that were deferred in order to get more information.
+/// Finalize this patch application, consuming the context, applying any
+/// deferred property updates, and returning the finally applied patch set.
 ///
 /// Ref properties from snapshots refer to eachother via snapshot ID. Some of
 /// these properties are transformed when the patch is computed, notably the
@@ -45,7 +44,7 @@ struct PatchApplyContext {
 /// The remaining Ref properties need to be handled during patch application,
 /// where we build up a map of snapshot IDs to instance IDs as they're created,
 /// then apply properties all at once at the end.
-fn apply_deferred_properties(context: PatchApplyContext, tree: &mut RojoTree) {
+fn finalize_patch_application(context: PatchApplyContext, tree: &mut RojoTree) -> AppliedPatchSet {
     for (id, mut properties) in context.properties_to_apply {
         let mut instance = tree
             .get_instance_mut(id)
@@ -63,6 +62,20 @@ fn apply_deferred_properties(context: PatchApplyContext, tree: &mut RojoTree) {
 
         *instance.properties_mut() = properties;
     }
+
+    context.applied_patch_set
+}
+
+fn apply_remove_instance(context: &mut PatchApplyContext, tree: &mut RojoTree, removed_id: RbxId) {
+    match tree.remove_instance(removed_id) {
+        Some(_) => context.applied_patch_set.removed.push(removed_id),
+        None => {
+            log::warn!(
+                "Patch application error: Tried to remove instance {} but it did not exist.",
+                removed_id
+            );
+        }
+    }
 }
 
 fn apply_add_child(
@@ -98,7 +111,7 @@ fn apply_add_child(
     }
 }
 
-fn apply_update_child(context: &PatchApplyContext, tree: &mut RojoTree, patch: PatchUpdate) {
+fn apply_update_child(context: &mut PatchApplyContext, tree: &mut RojoTree, patch: PatchUpdate) {
     if let Some(metadata) = patch.changed_metadata {
         tree.update_metadata(patch.id, metadata);
     }