diff --git a/TODO.md b/TODO.md
index b15aefb..9f7b742 100644
--- a/TODO.md
+++ b/TODO.md
@@ -1,4 +1,3 @@
 - better .cargo/bin handling:
   - get a list of all the files on "pre"/"restore"
   - move the files out of the way on "post"/"save" and move them back afterwards
-- properly clean sparse registry
diff --git a/dist/restore/index.js b/dist/restore/index.js
index 2d879ff..ce4b6d7 100644
--- a/dist/restore/index.js
+++ b/dist/restore/index.js
@@ -66810,6 +66810,16 @@ var exec = __nccwpck_require__(1514);
 
 
 
+function reportError(e) {
+    const { commandFailed } = e;
+    if (commandFailed) {
+        lib_core.error(`Command failed: ${commandFailed.command}`);
+        lib_core.error(commandFailed.stderr);
+    }
+    else {
+        lib_core.error(`${e.stack}`);
+    }
+}
 async function getCmdOutput(cmd, args = [], options = {}) {
     let stdout = "";
     let stderr = "";
@@ -66828,8 +66838,10 @@ async function getCmdOutput(cmd, args = [], options = {}) {
         });
     }
     catch (e) {
-        lib_core.error(`Command failed: ${cmd} ${args.join(" ")}`);
-        lib_core.error(stderr);
+        e.commandFailed = {
+            command: `${cmd} ${args.join(" ")}`,
+            stderr,
+        };
         throw e;
     }
     return stdout;
@@ -66837,10 +66849,10 @@ async function getCmdOutput(cmd, args = [], options = {}) {
 function getCacheHandler() {
     const cacheProvider = lib_core.getInput("cache-provider");
     switch (cacheProvider) {
-        case 'github':
+        case "github":
             lib_core.info("Using Github Cache.");
             return lib_cache;
-        case 'buildjet':
+        case "buildjet":
             lib_core.info("Using Buildjet Cache.");
             return cache;
         default:
@@ -67259,10 +67271,8 @@ async function cleanBin(oldBins) {
     }
 }
 async function cleanRegistry(packages, crates = true) {
-    // `.cargo/registry/src`
-    // we can remove this completely, as cargo will recreate this from `cache`
-    await rmRF(path.join(CARGO_HOME, "registry", "src"));
     // `.cargo/registry/index`
+    let pkgSet = new Set(packages.map((p) => p.name));
     const indexDir = await fs.promises.opendir(path.join(CARGO_HOME, "registry", "index"));
     for await (const dirent of indexDir) {
         if (dirent.isDirectory()) {
@@ -67273,15 +67283,35 @@ async function cleanRegistry(packages, crates = true) {
             if (await exists(path.join(dirPath, ".git"))) {
                 await rmRF(path.join(dirPath, ".cache"));
             }
-            // TODO: else, clean `.cache` based on the `packages`
+            else {
+                await cleanRegistryIndexCache(dirPath, pkgSet);
+            }
         }
     }
     if (!crates) {
-        core.debug(`skipping crate cleanup`);
+        core.debug("skipping registry cache and src cleanup");
         return;
     }
-    const pkgSet = new Set(packages.map((p) => `${p.name}-${p.version}.crate`));
+    // `.cargo/registry/src`
+    // Cargo usually re-creates these from the `.crate` cache below,
+    // but for some reason that does not work for `-sys` crates that check timestamps
+    // to decide if rebuilds are necessary.
+    pkgSet = new Set(packages.filter((p) => p.name.endsWith("-sys")).map((p) => `${p.name}-${p.version}`));
+    const srcDir = await fs.promises.opendir(path.join(CARGO_HOME, "registry", "src"));
+    for await (const dirent of srcDir) {
+        if (dirent.isDirectory()) {
+            // eg `.cargo/registry/src/github.com-1ecc6299db9ec823`
+            // or `.cargo/registry/src/index.crates.io-e139d0d48fed7772`
+            const dir = await fs.promises.opendir(path.join(srcDir.path, dirent.name));
+            for await (const dirent of dir) {
+                if (dirent.isDirectory() && !pkgSet.has(dirent.name)) {
+                    await rmRF(path.join(dir.path, dirent.name));
+                }
+            }
+        }
+    }
     // `.cargo/registry/cache`
+    pkgSet = new Set(packages.map((p) => `${p.name}-${p.version}.crate`));
     const cacheDir = await fs.promises.opendir(path.join(CARGO_HOME, "registry", "cache"));
     for await (const dirent of cacheDir) {
         if (dirent.isDirectory()) {
@@ -67297,6 +67327,30 @@ async function cleanRegistry(packages, crates = true) {
         }
     }
 }
+/// Recursively walks and cleans the index `.cache`
+async function cleanRegistryIndexCache(dirName, keepPkg) {
+    let dirIsEmpty = true;
+    const cacheDir = await fs.promises.opendir(dirName);
+    for await (const dirent of cacheDir) {
+        if (dirent.isDirectory()) {
+            if (await cleanRegistryIndexCache(path.join(dirName, dirent.name), keepPkg)) {
+                await rm(dirName, dirent);
+            }
+            else {
+                dirIsEmpty && (dirIsEmpty = false);
+            }
+        }
+        else {
+            if (keepPkg.has(dirent.name)) {
+                dirIsEmpty && (dirIsEmpty = false);
+            }
+            else {
+                await rm(dirName, dirent);
+            }
+        }
+    }
+    return dirIsEmpty;
+}
 async function cleanGit(packages) {
     const coPath = path.join(CARGO_HOME, "git", "checkouts");
     const dbPath = path.join(CARGO_HOME, "git", "db");
@@ -67466,7 +67520,7 @@ async function run() {
     }
     catch (e) {
         setCacheHitOutput(false);
-        lib_core.error(`${e.stack}`);
+        reportError(e);
     }
 }
 function setCacheHitOutput(cacheHit) {
diff --git a/dist/save/index.js b/dist/save/index.js
index 1979b19..35d72e1 100644
--- a/dist/save/index.js
+++ b/dist/save/index.js
@@ -66810,6 +66810,16 @@ var lib_cache = __nccwpck_require__(7799);
 
 
 
+function reportError(e) {
+    const { commandFailed } = e;
+    if (commandFailed) {
+        core.error(`Command failed: ${commandFailed.command}`);
+        core.error(commandFailed.stderr);
+    }
+    else {
+        core.error(`${e.stack}`);
+    }
+}
 async function getCmdOutput(cmd, args = [], options = {}) {
     let stdout = "";
     let stderr = "";
@@ -66828,8 +66838,10 @@ async function getCmdOutput(cmd, args = [], options = {}) {
         });
     }
     catch (e) {
-        core.error(`Command failed: ${cmd} ${args.join(" ")}`);
-        core.error(stderr);
+        e.commandFailed = {
+            command: `${cmd} ${args.join(" ")}`,
+            stderr,
+        };
         throw e;
     }
     return stdout;
@@ -66837,10 +66849,10 @@ async function getCmdOutput(cmd, args = [], options = {}) {
 function getCacheHandler() {
     const cacheProvider = core.getInput("cache-provider");
     switch (cacheProvider) {
-        case 'github':
+        case "github":
             core.info("Using Github Cache.");
             return lib_cache;
-        case 'buildjet':
+        case "buildjet":
             core.info("Using Buildjet Cache.");
             return cache;
         default:
@@ -67259,10 +67271,8 @@ async function cleanBin(oldBins) {
     }
 }
 async function cleanRegistry(packages, crates = true) {
-    // `.cargo/registry/src`
-    // we can remove this completely, as cargo will recreate this from `cache`
-    await rmRF(external_path_default().join(CARGO_HOME, "registry", "src"));
     // `.cargo/registry/index`
+    let pkgSet = new Set(packages.map((p) => p.name));
     const indexDir = await external_fs_default().promises.opendir(external_path_default().join(CARGO_HOME, "registry", "index"));
     for await (const dirent of indexDir) {
         if (dirent.isDirectory()) {
@@ -67273,15 +67283,35 @@ async function cleanRegistry(packages, crates = true) {
             if (await exists(external_path_default().join(dirPath, ".git"))) {
                 await rmRF(external_path_default().join(dirPath, ".cache"));
             }
-            // TODO: else, clean `.cache` based on the `packages`
+            else {
+                await cleanRegistryIndexCache(dirPath, pkgSet);
+            }
         }
     }
     if (!crates) {
-        core.debug(`skipping crate cleanup`);
+        core.debug("skipping registry cache and src cleanup");
         return;
     }
-    const pkgSet = new Set(packages.map((p) => `${p.name}-${p.version}.crate`));
+    // `.cargo/registry/src`
+    // Cargo usually re-creates these from the `.crate` cache below,
+    // but for some reason that does not work for `-sys` crates that check timestamps
+    // to decide if rebuilds are necessary.
+    pkgSet = new Set(packages.filter((p) => p.name.endsWith("-sys")).map((p) => `${p.name}-${p.version}`));
+    const srcDir = await external_fs_default().promises.opendir(external_path_default().join(CARGO_HOME, "registry", "src"));
+    for await (const dirent of srcDir) {
+        if (dirent.isDirectory()) {
+            // eg `.cargo/registry/src/github.com-1ecc6299db9ec823`
+            // or `.cargo/registry/src/index.crates.io-e139d0d48fed7772`
+            const dir = await external_fs_default().promises.opendir(external_path_default().join(srcDir.path, dirent.name));
+            for await (const dirent of dir) {
+                if (dirent.isDirectory() && !pkgSet.has(dirent.name)) {
+                    await rmRF(external_path_default().join(dir.path, dirent.name));
+                }
+            }
+        }
+    }
     // `.cargo/registry/cache`
+    pkgSet = new Set(packages.map((p) => `${p.name}-${p.version}.crate`));
     const cacheDir = await external_fs_default().promises.opendir(external_path_default().join(CARGO_HOME, "registry", "cache"));
     for await (const dirent of cacheDir) {
         if (dirent.isDirectory()) {
@@ -67297,6 +67327,30 @@ async function cleanRegistry(packages, crates = true) {
         }
     }
 }
+/// Recursively walks and cleans the index `.cache`
+async function cleanRegistryIndexCache(dirName, keepPkg) {
+    let dirIsEmpty = true;
+    const cacheDir = await external_fs_default().promises.opendir(dirName);
+    for await (const dirent of cacheDir) {
+        if (dirent.isDirectory()) {
+            if (await cleanRegistryIndexCache(external_path_default().join(dirName, dirent.name), keepPkg)) {
+                await rm(dirName, dirent);
+            }
+            else {
+                dirIsEmpty && (dirIsEmpty = false);
+            }
+        }
+        else {
+            if (keepPkg.has(dirent.name)) {
+                dirIsEmpty && (dirIsEmpty = false);
+            }
+            else {
+                await rm(dirName, dirent);
+            }
+        }
+    }
+    return dirIsEmpty;
+}
 async function cleanGit(packages) {
     const coPath = external_path_default().join(CARGO_HOME, "git", "checkouts");
     const dbPath = external_path_default().join(CARGO_HOME, "git", "db");
@@ -67446,7 +67500,7 @@ async function run() {
                 await cleanTargetDir(workspace.target, packages);
             }
             catch (e) {
-                core.error(`${e.stack}`);
+                core.debug(`${e.stack}`);
             }
         }
         try {
@@ -67455,21 +67509,21 @@ async function run() {
             await cleanRegistry(allPackages, crates !== "true");
         }
         catch (e) {
-            core.error(`${e.stack}`);
+            core.debug(`${e.stack}`);
         }
         try {
             core.info(`... Cleaning cargo/bin ...`);
             await cleanBin(config.cargoBins);
         }
         catch (e) {
-            core.error(`${e.stack}`);
+            core.debug(`${e.stack}`);
         }
         try {
             core.info(`... Cleaning cargo git cache ...`);
             await cleanGit(allPackages);
         }
         catch (e) {
-            core.error(`${e.stack}`);
+            core.debug(`${e.stack}`);
         }
         core.info(`... Saving cache ...`);
         // Pass a copy of cachePaths to avoid mutating the original array as reported by:
@@ -67478,7 +67532,7 @@ async function run() {
         await cache.saveCache(config.cachePaths.slice(), config.cacheKey);
     }
     catch (e) {
-        core.error(`${e.stack}`);
+        reportError(e);
     }
 }
 run();
diff --git a/src/cleanup.ts b/src/cleanup.ts
index 9f65366..6f7327c 100644
--- a/src/cleanup.ts
+++ b/src/cleanup.ts
@@ -91,11 +91,8 @@ export async function cleanBin(oldBins: Array<string>) {
 }
 
 export async function cleanRegistry(packages: Packages, crates = true) {
-  // `.cargo/registry/src`
-  // we can remove this completely, as cargo will recreate this from `cache`
-  await rmRF(path.join(CARGO_HOME, "registry", "src"));
-
   // `.cargo/registry/index`
+  let pkgSet = new Set(packages.map((p) => p.name));
   const indexDir = await fs.promises.opendir(path.join(CARGO_HOME, "registry", "index"));
   for await (const dirent of indexDir) {
     if (dirent.isDirectory()) {
@@ -106,19 +103,38 @@ export async function cleanRegistry(packages: Packages, crates = true) {
       // for a git registry, we can remove `.cache`, as cargo will recreate it from git
       if (await exists(path.join(dirPath, ".git"))) {
         await rmRF(path.join(dirPath, ".cache"));
+      } else {
+        await cleanRegistryIndexCache(dirPath, pkgSet);
       }
-      // TODO: else, clean `.cache` based on the `packages`
     }
   }
 
   if (!crates) {
-    core.debug(`skipping crate cleanup`);
+    core.debug("skipping registry cache and src cleanup");
     return;
   }
 
-  const pkgSet = new Set(packages.map((p) => `${p.name}-${p.version}.crate`));
+  // `.cargo/registry/src`
+  // Cargo usually re-creates these from the `.crate` cache below,
+  // but for some reason that does not work for `-sys` crates that check timestamps
+  // to decide if rebuilds are necessary.
+  pkgSet = new Set(packages.filter((p) => p.name.endsWith("-sys")).map((p) => `${p.name}-${p.version}`));
+  const srcDir = await fs.promises.opendir(path.join(CARGO_HOME, "registry", "src"));
+  for await (const dirent of srcDir) {
+    if (dirent.isDirectory()) {
+      // eg `.cargo/registry/src/github.com-1ecc6299db9ec823`
+      // or `.cargo/registry/src/index.crates.io-e139d0d48fed7772`
+      const dir = await fs.promises.opendir(path.join(srcDir.path, dirent.name));
+      for await (const dirent of dir) {
+        if (dirent.isDirectory() && !pkgSet.has(dirent.name)) {
+          await rmRF(path.join(dir.path, dirent.name));
+        }
+      }
+    }
+  }
 
   // `.cargo/registry/cache`
+  pkgSet = new Set(packages.map((p) => `${p.name}-${p.version}.crate`));
   const cacheDir = await fs.promises.opendir(path.join(CARGO_HOME, "registry", "cache"));
   for await (const dirent of cacheDir) {
     if (dirent.isDirectory()) {
@@ -135,6 +151,28 @@ export async function cleanRegistry(packages: Packages, crates = true) {
   }
 }
 
+/// Recursively walks and cleans the index `.cache`
+async function cleanRegistryIndexCache(dirName: string, keepPkg: Set<string>) {
+  let dirIsEmpty = true;
+  const cacheDir = await fs.promises.opendir(dirName);
+  for await (const dirent of cacheDir) {
+    if (dirent.isDirectory()) {
+      if (await cleanRegistryIndexCache(path.join(dirName, dirent.name), keepPkg)) {
+        await rm(dirName, dirent);
+      } else {
+        dirIsEmpty &&= false;
+      }
+    } else {
+      if (keepPkg.has(dirent.name)) {
+        dirIsEmpty &&= false;
+      } else {
+        await rm(dirName, dirent);
+      }
+    }
+  }
+  return dirIsEmpty;
+}
+
 export async function cleanGit(packages: Packages) {
   const coPath = path.join(CARGO_HOME, "git", "checkouts");
   const dbPath = path.join(CARGO_HOME, "git", "db");
diff --git a/src/restore.ts b/src/restore.ts
index 2c10a03..577324a 100644
--- a/src/restore.ts
+++ b/src/restore.ts
@@ -2,7 +2,7 @@ import * as core from "@actions/core";
 
 import { cleanTargetDir } from "./cleanup";
 import { CacheConfig } from "./config";
-import { getCacheHandler } from "./utils";
+import { getCacheHandler, reportError } from "./utils";
 
 process.on("uncaughtException", (e) => {
   core.error(e.message);
@@ -62,7 +62,7 @@ async function run() {
   } catch (e) {
     setCacheHitOutput(false);
 
-    core.error(`${(e as any).stack}`);
+    reportError(e);
   }
 }
 
diff --git a/src/save.ts b/src/save.ts
index cb9113a..77d4e11 100644
--- a/src/save.ts
+++ b/src/save.ts
@@ -3,7 +3,7 @@ import * as exec from "@actions/exec";
 
 import { cleanBin, cleanGit, cleanRegistry, cleanTargetDir } from "./cleanup";
 import { CacheConfig, isCacheUpToDate } from "./config";
-import { getCacheHandler } from "./utils";
+import { getCacheHandler, reportError } from "./utils";
 
 process.on("uncaughtException", (e) => {
   core.error(e.message);
@@ -42,30 +42,30 @@ async function run() {
         core.info(`... Cleaning ${workspace.target} ...`);
         await cleanTargetDir(workspace.target, packages);
       } catch (e) {
-        core.error(`${(e as any).stack}`);
+        core.debug(`${(e as any).stack}`);
       }
     }
 
     try {
-      const crates = core.getInput("cache-all-crates").toLowerCase() || "false"
+      const crates = core.getInput("cache-all-crates").toLowerCase() || "false";
       core.info(`... Cleaning cargo registry cache-all-crates: ${crates} ...`);
       await cleanRegistry(allPackages, crates !== "true");
     } catch (e) {
-      core.error(`${(e as any).stack}`);
+      core.debug(`${(e as any).stack}`);
     }
 
     try {
       core.info(`... Cleaning cargo/bin ...`);
       await cleanBin(config.cargoBins);
     } catch (e) {
-      core.error(`${(e as any).stack}`);
+      core.debug(`${(e as any).stack}`);
     }
 
     try {
       core.info(`... Cleaning cargo git cache ...`);
       await cleanGit(allPackages);
     } catch (e) {
-      core.error(`${(e as any).stack}`);
+      core.debug(`${(e as any).stack}`);
     }
 
     core.info(`... Saving cache ...`);
@@ -74,7 +74,7 @@ async function run() {
     // TODO: remove this once the underlying bug is fixed.
     await cache.saveCache(config.cachePaths.slice(), config.cacheKey);
   } catch (e) {
-    core.error(`${(e as any).stack}`);
+    reportError(e);
   }
 }
 
diff --git a/src/utils.ts b/src/utils.ts
index 7dafd9c..3751dd8 100644
--- a/src/utils.ts
+++ b/src/utils.ts
@@ -3,6 +3,16 @@ import * as ghCache from "@actions/cache";
 import * as core from "@actions/core";
 import * as exec from "@actions/exec";
 
+export function reportError(e: any) {
+  const { commandFailed } = e;
+  if (commandFailed) {
+    core.error(`Command failed: ${commandFailed.command}`);
+    core.error(commandFailed.stderr);
+  } else {
+    core.error(`${e.stack}`);
+  }
+}
+
 export async function getCmdOutput(
   cmd: string,
   args: Array<string> = [],
@@ -24,23 +34,25 @@ export async function getCmdOutput(
       ...options,
     });
   } catch (e) {
-    core.error(`Command failed: ${cmd} ${args.join(" ")}`);
-    core.error(stderr);
+    (e as any).commandFailed = {
+      command: `${cmd} ${args.join(" ")}`,
+      stderr,
+    };
     throw e;
   }
   return stdout;
 }
 
 export function getCacheHandler() {
-    const cacheProvider = core.getInput("cache-provider");
-    switch (cacheProvider) {
-      case 'github':
-        core.info ("Using Github Cache.");
-        return ghCache;
-      case 'buildjet':
-        core.info ("Using Buildjet Cache.");
-        return buildjetCache;
-      default:
-        throw new Error("Only currently support github and buildjet caches");
-    }
+  const cacheProvider = core.getInput("cache-provider");
+  switch (cacheProvider) {
+    case "github":
+      core.info("Using Github Cache.");
+      return ghCache;
+    case "buildjet":
+      core.info("Using Buildjet Cache.");
+      return buildjetCache;
+    default:
+      throw new Error("Only currently support github and buildjet caches");
+  }
 }