From cb97257cc5c333af3ca95c81d978df939a7bda84 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Tue, 21 Jul 2026 10:35:46 -0700
Subject: [PATCH 1/5] Fix bug with traversing extracted packages when cleaning
 tarballs

---
 libmamba/src/api/clean.cpp     | 17 +++++++++++----
 micromamba/tests/test_clean.py | 38 ++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 4 deletions(-)

diff --git a/libmamba/src/api/clean.cpp b/libmamba/src/api/clean.cpp
index 1e542ef073..e4f40132ef 100644
--- a/libmamba/src/api/clean.cpp
+++ b/libmamba/src/api/clean.cpp
@@ -233,21 +233,30 @@ namespace mamba
                      ++it)
                 {
                     const auto& p = *it;
+                    if (p.is_symlink())
+                    {
+                        continue;
+                    }
                     if (p.is_directory())
                     {
-                        if (is_inside_cache_metadata(p.path(), cache_root))
+                        const bool is_extracted_package = fs::exists(
+                            p.path() / "info" / "index.json"
+                        );
+                        if (is_inside_cache_metadata(p.path(), cache_root)
+                            || is_extracted_package)
                         {
                             it.disable_recursion_pending();
                         }
                         continue;
                     }
-                    if (!p.is_directory()
+                    if (p.is_regular_file()
                         && (util::ends_with(p.path().string(), ".tar.bz2")
                             || util::ends_with(p.path().string(), ".conda")))
                     {
+                        const auto size = p.file_size();
                         res.push_back(p.path());
-                        rows.push_back({ p.path().filename().string(), get_file_size(p.file_size()) });
-                        total_size += p.file_size();
+                        rows.push_back({ p.path().filename().string(), get_file_size(size) });
+                        total_size += size;
                     }
                 }
                 std::sort(
diff --git a/micromamba/tests/test_clean.py b/micromamba/tests/test_clean.py
index 95e0954245..d7717f1f67 100644
--- a/micromamba/tests/test_clean.py
+++ b/micromamba/tests/test_clean.py
@@ -43,6 +43,44 @@ def test_clean_all_removes_nested_package_cache_entries(tmp_home, tmp_root_prefi
     assert not extracted.exists()
 
 
+def test_clean_tarballs_does_not_enter_extracted_packages(tmp_home, tmp_root_prefix):
+    pkgs_dir = tmp_home / "pkgs"
+    os.environ["CONDA_PKGS_DIRS"] = str(pkgs_dir)
+
+    channel_dir = pkgs_dir / "https" / "conda.anaconda.org" / "conda-forge" / "linux-64"
+    channel_dir.mkdir(parents=True, exist_ok=True)
+
+    tarball = channel_dir / "ambertools-26.0-test.conda"
+    tarball.write_bytes(b"cached package archive")
+
+    extracted = channel_dir / "ambertools-26.0-test"
+    (extracted / "info").mkdir(parents=True)
+    (extracted / "info" / "index.json").write_text("{}")
+
+    payload_file = extracted / "share" / "example.conda"
+    payload_file.parent.mkdir(parents=True)
+    payload_file.write_bytes(b"package payload")
+
+    # AmberTools ships a bin/amber.conda symlink. On conda-forge it can be
+    # dangling because the package does not include Amber's bundled Miniconda.
+    # Creating symlinks may require elevated privileges on Windows, so the
+    # regular payload file above provides cross-platform coverage.
+    dangling_symlink = None
+    if os.name != "nt":
+        dangling_symlink = extracted / "bin" / "amber.conda"
+        dangling_symlink.parent.mkdir()
+        dangling_symlink.symlink_to("../miniconda/bin/conda")
+        assert dangling_symlink.is_symlink()
+
+    helpers.clean("--tarballs", "--no-rc", no_dry_run=True)
+
+    assert not tarball.exists()
+    assert extracted.exists()
+    assert payload_file.exists()
+    if dangling_symlink is not None:
+        assert dangling_symlink.is_symlink()
+
+
 def test_clean_all_clears_all_cache_kinds(tmp_home, tmp_root_prefix):
     pkgs_dir = tmp_home / "pkgs"
     os.environ["CONDA_PKGS_DIRS"] = str(pkgs_dir)

From ecd94b1bed26fff84c7d623caf2f3c2c1adf1ba4 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Tue, 21 Jul 2026 10:42:03 -0700
Subject: [PATCH 2/5] fix issue with clang format

---
 libmamba/src/api/clean.cpp | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/libmamba/src/api/clean.cpp b/libmamba/src/api/clean.cpp
index e4f40132ef..9ca6cc37f1 100644
--- a/libmamba/src/api/clean.cpp
+++ b/libmamba/src/api/clean.cpp
@@ -239,11 +239,8 @@ namespace mamba
                     }
                     if (p.is_directory())
                     {
-                        const bool is_extracted_package = fs::exists(
-                            p.path() / "info" / "index.json"
-                        );
-                        if (is_inside_cache_metadata(p.path(), cache_root)
-                            || is_extracted_package)
+                        const bool is_extracted_package = fs::exists(p.path() / "info" / "index.json");
+                        if (is_inside_cache_metadata(p.path(), cache_root) || is_extracted_package)
                         {
                             it.disable_recursion_pending();
                         }

From 8b4628c2a0d5feefe14fbfd2d153fd7447709afe Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Tue, 28 Jul 2026 14:41:46 -0700
Subject: [PATCH 3/5] thanks for the feedback @jjerphan

---
 libmamba/src/api/clean.cpp     | 11 +++--------
 micromamba/tests/test_clean.py |  4 ++--
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/libmamba/src/api/clean.cpp b/libmamba/src/api/clean.cpp
index 9ca6cc37f1..8d29afb647 100644
--- a/libmamba/src/api/clean.cpp
+++ b/libmamba/src/api/clean.cpp
@@ -233,14 +233,10 @@ namespace mamba
                      ++it)
                 {
                     const auto& p = *it;
-                    if (p.is_symlink())
-                    {
-                        continue;
-                    }
                     if (p.is_directory())
                     {
                         const bool is_extracted_package = fs::exists(p.path() / "info" / "index.json");
-                        if (is_inside_cache_metadata(p.path(), cache_root) || is_extracted_package)
+                        if (is_extracted_package || is_inside_cache_metadata(p.path(), cache_root))
                         {
                             it.disable_recursion_pending();
                         }
@@ -250,10 +246,9 @@ namespace mamba
                         && (util::ends_with(p.path().string(), ".tar.bz2")
                             || util::ends_with(p.path().string(), ".conda")))
                     {
-                        const auto size = p.file_size();
                         res.push_back(p.path());
-                        rows.push_back({ p.path().filename().string(), get_file_size(size) });
-                        total_size += size;
+                        rows.push_back({ p.path().filename().string(), get_file_size(p.file_size()) });
+                        total_size += p.file_size();
                     }
                 }
                 std::sort(
diff --git a/micromamba/tests/test_clean.py b/micromamba/tests/test_clean.py
index d7717f1f67..fc73524360 100644
--- a/micromamba/tests/test_clean.py
+++ b/micromamba/tests/test_clean.py
@@ -43,9 +43,9 @@ def test_clean_all_removes_nested_package_cache_entries(tmp_home, tmp_root_prefi
     assert not extracted.exists()
 
 
-def test_clean_tarballs_does_not_enter_extracted_packages(tmp_home, tmp_root_prefix):
+def test_clean_tarballs_does_not_enter_extracted_packages(tmp_home, tmp_root_prefix, monkeypatch):
     pkgs_dir = tmp_home / "pkgs"
-    os.environ["CONDA_PKGS_DIRS"] = str(pkgs_dir)
+    monkeypatch.setenv("CONDA_PKGS_DIRS", str(pkgs_dir))
 
     channel_dir = pkgs_dir / "https" / "conda.anaconda.org" / "conda-forge" / "linux-64"
     channel_dir.mkdir(parents=True, exist_ok=True)

From c180b62545adf551b92229c8547b80bbf8506b91 Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Wed, 29 Jul 2026 14:19:34 -0700
Subject: [PATCH 4/5] thanks for the feedback again @jjerphan

---
 libmamba/src/api/clean.cpp     | 2 +-
 micromamba/tests/test_clean.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/libmamba/src/api/clean.cpp b/libmamba/src/api/clean.cpp
index 8d29afb647..d069735e50 100644
--- a/libmamba/src/api/clean.cpp
+++ b/libmamba/src/api/clean.cpp
@@ -242,7 +242,7 @@ namespace mamba
                         }
                         continue;
                     }
-                    if (p.is_regular_file()
+                    if (!p.is_directory()
                         && (util::ends_with(p.path().string(), ".tar.bz2")
                             || util::ends_with(p.path().string(), ".conda")))
                     {
diff --git a/micromamba/tests/test_clean.py b/micromamba/tests/test_clean.py
index fc73524360..7a4396c183 100644
--- a/micromamba/tests/test_clean.py
+++ b/micromamba/tests/test_clean.py
@@ -66,7 +66,7 @@ def test_clean_tarballs_does_not_enter_extracted_packages(tmp_home, tmp_root_pre
     # Creating symlinks may require elevated privileges on Windows, so the
     # regular payload file above provides cross-platform coverage.
     dangling_symlink = None
-    if os.name != "nt":
+    if platform.system() != "Windows":
         dangling_symlink = extracted / "bin" / "amber.conda"
         dangling_symlink.parent.mkdir()
         dangling_symlink.symlink_to("../miniconda/bin/conda")

From a0f9d5d3b5253e5a6ecdc58272091da7d94dd2ce Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Wed, 29 Jul 2026 14:20:28 -0700
Subject: [PATCH 5/5] forgot import

---
 micromamba/tests/test_clean.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/micromamba/tests/test_clean.py b/micromamba/tests/test_clean.py
index 7a4396c183..650e361b57 100644
--- a/micromamba/tests/test_clean.py
+++ b/micromamba/tests/test_clean.py
@@ -1,4 +1,5 @@
 import os
+import platform
 
 from .helpers import *  # noqa: F403
 from . import helpers