diff --git a/.authors.yml b/.authors.yml
index 6b71ac9dc7..dc7b1a4258 100644
--- a/.authors.yml
+++ b/.authors.yml
@@ -612,7 +612,7 @@
   first_commit: 2015-08-30 06:44:37
 - name: Marcel Bargull
   email: marcel.bargull@udo.edu
-  num_commits: 80
+  num_commits: 82
   first_commit: 2016-09-26 11:45:54
   github: mbargull
   alternate_emails:
@@ -1202,7 +1202,7 @@
   alternate_emails:
   - clee@anaconda.com
 - name: Ken Odegard
-  num_commits: 167
+  num_commits: 168
   email: kodegard@anaconda.com
   first_commit: 2020-09-08 19:53:41
   github: kenodegard
diff --git a/CHANGELOG.md b/CHANGELOG.md
index dfe35b2345..840bc6636a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,18 @@
 [//]: # (current developments)
 
+## 24.1.2 (2024-02-15)
+
+### Bug fixes
+
+* Fix rpaths patcher being run on symbolic links. (#5179 via #5181)
+* Fix corrupted package cache for outputs in subpackage tests. (#5184)
+
+### Contributors
+
+* @mbargull
+
+
+
 ## 24.1.1 (2024-02-07)
 
 ### Bug fixes
diff --git a/conda_build/build.py b/conda_build/build.py
index 28ffc04a70..526d665c8a 100644
--- a/conda_build/build.py
+++ b/conda_build/build.py
@@ -38,6 +38,7 @@
     env_path_backup_var_exists,
     get_conda_channel,
     get_rc_urls,
+    pkgs_dirs,
     prefix_placeholder,
     reset_context,
     root_dir,
@@ -3394,6 +3395,25 @@ def test(
     #     folder destination
     _extract_test_files_from_package(metadata)
 
+    # Remove any previously cached build from the package cache to ensure we
+    # really test the requested build and not some clashing or corrupted build.
+    # (Corruption of the extracted package can happen, e.g., in multi-output
+    # builds if one of the subpackages overwrites files from the other.)
+    # Special case:
+    #   If test is requested for .tar.bz2/.conda file from the pkgs dir itself,
+    #   clean_pkg_cache() will remove it; don't call that function in this case.
+    in_pkg_cache = (
+        not hasattr(recipedir_or_package_or_metadata, "config")
+        and os.path.isfile(recipedir_or_package_or_metadata)
+        and recipedir_or_package_or_metadata.endswith(CONDA_PACKAGE_EXTENSIONS)
+        and any(
+            os.path.dirname(recipedir_or_package_or_metadata) in pkgs_dir
+            for pkgs_dir in pkgs_dirs
+        )
+    )
+    if not in_pkg_cache:
+        environ.clean_pkg_cache(metadata.dist(), metadata.config)
+
     copy_test_source_files(metadata, metadata.config.test_dir)
     # this is also copying tests/source_files from work_dir to testing workdir
 
diff --git a/conda_build/environ.py b/conda_build/environ.py
index 3026f1bf60..762b9c7479 100644
--- a/conda_build/environ.py
+++ b/conda_build/environ.py
@@ -16,10 +16,15 @@
 from logging import getLogger
 from os.path import join, normpath
 
-from conda.base.constants import DEFAULTS_CHANNEL_NAME, UNKNOWN_CHANNEL
+from conda.base.constants import (
+    CONDA_PACKAGE_EXTENSIONS,
+    DEFAULTS_CHANNEL_NAME,
+    UNKNOWN_CHANNEL,
+)
 from conda.common.io import env_vars
 from conda.core.index import LAST_CHANNEL_URLS
 from conda.core.link import PrefixSetup, UnlinkLinkTransaction
+from conda.core.package_cache_data import PackageCacheData
 from conda.core.prefix_data import PrefixData
 from conda.models.channel import prioritize_channels
 
@@ -43,6 +48,7 @@
     reset_context,
     root_dir,
 )
+from .config import Config
 from .deprecations import deprecated
 from .exceptions import BuildLockError, DependencyNeedsBuildingError
 from .features import feature_list
@@ -1264,6 +1270,29 @@ def get_pkg_dirs_locks(dirs, config):
     return [utils.get_lock(folder, timeout=config.timeout) for folder in dirs]
 
 
+def clean_pkg_cache(dist: str, config: Config) -> None:
+    with utils.LoggingContext(logging.DEBUG if config.debug else logging.WARN):
+        locks = get_pkg_dirs_locks([config.bldpkgs_dir] + pkgs_dirs, config)
+        with utils.try_acquire_locks(locks, timeout=config.timeout):
+            for pkgs_dir in pkgs_dirs:
+                if any(
+                    os.path.exists(os.path.join(pkgs_dir, f"{dist}{ext}"))
+                    for ext in ("", *CONDA_PACKAGE_EXTENSIONS)
+                ):
+                    log.debug(
+                        "Conda caching error: %s package remains in cache after removal",
+                        dist,
+                    )
+                    log.debug("manually removing to compensate")
+                    package_cache = PackageCacheData.first_writable([pkgs_dir])
+                    for cache_pkg_id in package_cache.query(dist):
+                        package_cache.remove(cache_pkg_id)
+
+        # Note that this call acquires the relevant locks, so this must be called
+        # outside the lock context above.
+        remove_existing_packages(pkgs_dirs, [dist], config)
+
+
 def remove_existing_packages(dirs, fns, config):
     locks = get_pkg_dirs_locks(dirs, config) if config.locking else []
 
diff --git a/conda_build/inspect_pkg.py b/conda_build/inspect_pkg.py
index 3f3fba7545..c5a1d92ec8 100644
--- a/conda_build/inspect_pkg.py
+++ b/conda_build/inspect_pkg.py
@@ -330,7 +330,7 @@ def inspect_objects(
         info = []
         for f in obj_files:
             path = join(prefix, f)
-            codefile = codefile_class(path)
+            codefile = codefile_class(path, skip_symlinks=True)
             if codefile == machofile:
                 info.append(
                     {
diff --git a/conda_build/os_utils/ldd.py b/conda_build/os_utils/ldd.py
index 3ab78bc7fd..c45def903e 100644
--- a/conda_build/os_utils/ldd.py
+++ b/conda_build/os_utils/ldd.py
@@ -111,11 +111,17 @@ def _get_linkages(
 def get_package_obj_files(
     prec: PrefixRecord, prefix: str | os.PathLike | Path
 ) -> list[str]:
-    return [file for file in prec["files"] if codefile_class(Path(prefix, file))]
+    return [
+        file
+        for file in prec["files"]
+        if codefile_class(Path(prefix, file), skip_symlinks=True)
+    ]
 
 
 @lru_cache(maxsize=None)
 def get_untracked_obj_files(prefix: str | os.PathLike | Path) -> list[str]:
     return [
-        file for file in untracked(str(prefix)) if codefile_class(Path(prefix, file))
+        file
+        for file in untracked(str(prefix))
+        if codefile_class(Path(prefix, file), skip_symlinks=True)
     ]
diff --git a/conda_build/os_utils/liefldd.py b/conda_build/os_utils/liefldd.py
index c44a03f864..cc365decdf 100644
--- a/conda_build/os_utils/liefldd.py
+++ b/conda_build/os_utils/liefldd.py
@@ -504,7 +504,8 @@ def inspect_linkages_lief(
                     while tmp_filename:
                         if (
                             not parent_exe_dirname
-                            and codefile_class(tmp_filename) == EXEfile
+                            and codefile_class(tmp_filename, skip_symlinks=True)
+                            == EXEfile
                         ):
                             parent_exe_dirname = os.path.dirname(tmp_filename)
                         tmp_filename = parents_by_filename[tmp_filename]
@@ -600,7 +601,8 @@ def get_linkages(
     result_pyldd = []
     debug = False
     if not have_lief or debug:
-        if codefile_class(filename) not in (DLLfile, EXEfile):
+        codefile = codefile_class(filename, skip_symlinks=True)
+        if codefile not in (DLLfile, EXEfile):
             result_pyldd = inspect_linkages_pyldd(
                 filename,
                 resolve_filenames=resolve_filenames,
@@ -612,7 +614,7 @@ def get_linkages(
                 return result_pyldd
         else:
             print(
-                f"WARNING: failed to get_linkages, codefile_class('{filename}')={codefile_class(filename)}"
+                f"WARNING: failed to get_linkages, codefile_class('{filename}', True)={codefile}"
             )
             return {}
     result_lief = inspect_linkages_lief(
diff --git a/conda_build/post.py b/conda_build/post.py
index 5a05eda077..3b9cb6c832 100644
--- a/conda_build/post.py
+++ b/conda_build/post.py
@@ -74,7 +74,7 @@
 
 def fix_shebang(f, prefix, build_python, osx_is_app=False):
     path = join(prefix, f)
-    if codefile_class(path):
+    if codefile_class(path, skip_symlinks=True):
         return
     elif islink(path):
         return
@@ -413,7 +413,7 @@ def osx_ch_link(path, link_dict, host_prefix, build_prefix, files):
             ".. seems to be linking to a compiler runtime, replacing build prefix with "
             "host prefix and"
         )
-        if not codefile_class(link):
+        if not codefile_class(link, skip_symlinks=True):
             sys.exit(
                 "Error: Compiler runtime library in build prefix not found in host prefix %s"
                 % link
@@ -653,7 +653,7 @@ def get_dsos(prec: PrefixRecord, prefix: str | os.PathLike | Path) -> set[str]:
     return {
         file
         for file in prec["files"]
-        if codefile_class(Path(prefix, file))
+        if codefile_class(Path(prefix, file), skip_symlinks=True)
         # codefile_class already filters by extension/binary type, do we need this second filter?
         for ext in (".dylib", ".so", ".dll", ".pyd")
         if ext in file
@@ -836,7 +836,7 @@ def _collect_needed_dsos(
         sysroots = list(sysroots_files.keys())[0]
     for f in files:
         path = join(run_prefix, f)
-        if not codefile_class(path):
+        if not codefile_class(path, skip_symlinks=True):
             continue
         build_prefix = build_prefix.replace(os.sep, "/")
         run_prefix = run_prefix.replace(os.sep, "/")
@@ -1174,7 +1174,7 @@ def _show_linking_messages(
             )
     for f in files:
         path = join(run_prefix, f)
-        codefile = codefile_class(path)
+        codefile = codefile_class(path, skip_symlinks=True)
         if codefile not in filetypes_for_platform[subdir.split("-")[0]]:
             continue
         warn_prelude = "WARNING ({},{})".format(pkg_name, f.replace(os.sep, "/"))
@@ -1273,7 +1273,7 @@ def check_overlinking_impl(
     filesu = []
     for file in files:
         path = join(run_prefix, file)
-        codefile = codefile_class(path)
+        codefile = codefile_class(path, skip_symlinks=True)
         if codefile in filetypes_for_platform[subdir.split("-")[0]]:
             files_to_inspect.append(file)
         filesu.append(file.replace("\\", "/"))
@@ -1578,7 +1578,7 @@ def post_process_shared_lib(m, f, files, host_prefix=None):
     if not host_prefix:
         host_prefix = m.config.host_prefix
     path = join(host_prefix, f)
-    codefile = codefile_class(path)
+    codefile = codefile_class(path, skip_symlinks=True)
     if not codefile or path.endswith(".debug"):
         return
     rpaths = m.get_value("build/rpaths", ["lib"])
@@ -1737,7 +1737,9 @@ def check_symlinks(files, prefix, croot):
             # symlinks to binaries outside of the same dir don't work.  RPATH stuff gets confused
             #    because ld.so follows symlinks in RPATHS
             #    If condition exists, then copy the file rather than symlink it.
-            if not dirname(link_path) == dirname(real_link_path) and codefile_class(f):
+            if not dirname(link_path) == dirname(real_link_path) and codefile_class(
+                f, skip_symlinks=True
+            ):
                 os.remove(path)
                 utils.copy_into(real_link_path, path)
             elif real_link_path.startswith(real_build_prefix):
diff --git a/pyproject.toml b/pyproject.toml
index 72f657031e..4ae5105a55 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,7 +31,7 @@ dependencies = [
   "beautifulsoup4",
   "chardet",
   "conda >=22.11",
-  "conda-index",
+  "conda-index >=0.4.0",
   "conda-package-handling >=1.3",
   "filelock",
   "jinja2",
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
index fb5088e15e..9b1ec2f3bc 100644
--- a/recipe/meta.yaml
+++ b/recipe/meta.yaml
@@ -31,7 +31,7 @@ requirements:
     - beautifulsoup4
     - chardet
     - conda >=22.11.0
-    - conda-index
+    - conda-index >=0.4.0
     - conda-package-handling >=1.3
     - filelock
     - jinja2
diff --git a/tests/test-recipes/metadata/_rpath_symlink/meta.yaml b/tests/test-recipes/metadata/_rpath_symlink/meta.yaml
new file mode 100644
index 0000000000..0ef58cdab2
--- /dev/null
+++ b/tests/test-recipes/metadata/_rpath_symlink/meta.yaml
@@ -0,0 +1,39 @@
+{% set lib_file = "libthing.so.1.0.0" %}  # [linux]
+{% set lib_file = "libthing.1.0.0.dylib" %}  # [osx]
+
+package:
+  name: rpath_symlink
+  version: 1.0.0
+
+build:
+  skip: true  # [not (linux or osx)]
+  rpaths_patcher: {{ rpaths_patcher }}
+  script:
+    - mkdir -p "${PREFIX}/lib"
+    - >
+      < /dev/null ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS}
+      -x c - -nostdlib -s -o "${PREFIX}/lib/{{ lib_file }}" "-Wl,-rpath,${PREFIX}/lib"
+      -shared -Wl,-soname,libthing.so.1  # [linux]
+      -dynamiclib -install_name libthing.1.dylib  # [osx]
+    - ln -s "${PREFIX}/lib/{{ lib_file }}" "${PREFIX}/lib/libthing.so.1"  # [linux]
+    - ln -s "${PREFIX}/lib/{{ lib_file }}" "${PREFIX}/lib/libthing.1.dylib"  # [osx]
+    - mkdir -p "${PREFIX}/lib/subfolder"
+    - ln -s "${PREFIX}/lib/{{ lib_file }}" "${PREFIX}/lib/subfolder/libthing-link.so"  # [linux]
+    - ln -s "${PREFIX}/lib/{{ lib_file }}" "${PREFIX}/lib/subfolder/libthing-link.dylib"  # [osx]
+
+requirements:
+  build:
+    - {{ compiler("c") }}
+
+test:
+  requires:
+    - py-lief
+  commands:
+    # Test that we get only a single entry that is the library's own directory.
+    - |
+      python -c '
+      import os, lief
+      lib = lief.parse(os.environ["PREFIX"] + "/lib/{{ lib_file }}")
+      assert {"$ORIGIN/."} == {e.rpath for e in lib.dynamic_entries if e.tag == lief.ELF.DYNAMIC_TAGS.RPATH}  # [linux]
+      assert {"@loader_path/"} == {command.path for command in lib.commands if command.command == lief.MachO.LOAD_COMMAND_TYPES.RPATH}  # [osx]
+      '
diff --git a/tests/test-recipes/metadata/outputs_overwrite_base_file/install.bat b/tests/test-recipes/metadata/outputs_overwrite_base_file/install.bat
new file mode 100644
index 0000000000..b6584f3971
--- /dev/null
+++ b/tests/test-recipes/metadata/outputs_overwrite_base_file/install.bat
@@ -0,0 +1,2 @@
+:: Always output 4 characters to properly test even if "SafetyError: ... incorrect size." is not triggered.
+< nul set /p="%PKG_NAME:~0,4%" > "%PREFIX%\file" & call;
diff --git a/tests/test-recipes/metadata/outputs_overwrite_base_file/install.sh b/tests/test-recipes/metadata/outputs_overwrite_base_file/install.sh
new file mode 100644
index 0000000000..cb0be8cb2b
--- /dev/null
+++ b/tests/test-recipes/metadata/outputs_overwrite_base_file/install.sh
@@ -0,0 +1,2 @@
+## Always output 4 characters to properly test even if "SafetyError: ... incorrect size." is not triggered.
+printf '%.4s' "${PKG_NAME}" > "${PREFIX}/file"
diff --git a/tests/test-recipes/metadata/outputs_overwrite_base_file/meta.yaml b/tests/test-recipes/metadata/outputs_overwrite_base_file/meta.yaml
new file mode 100644
index 0000000000..1c27afc126
--- /dev/null
+++ b/tests/test-recipes/metadata/outputs_overwrite_base_file/meta.yaml
@@ -0,0 +1,40 @@
+{% set name = "outputs_overwrite_base_file" %}
+
+package:
+  name: {{ name }}
+  version: 1.0
+
+outputs:
+  - name: base-{{ name }}
+    script: install.sh  # [unix]
+    script: install.bat  # [win]
+
+  - name: first-{{ name }}
+    script: install.sh  # [unix]
+    script: install.bat  # [win]
+    requirements:
+      host:
+        - {{ pin_subpackage("base-" + name) }}
+      run:
+        - {{ pin_subpackage("base-" + name) }}
+    test:
+      commands:
+        - content="$(cat "${PREFIX}/file")"  # [unix]
+        - test "${content}" = base  # [unix]
+        - < "%PREFIX%\file%" set /p content=  # [win]
+        - if not "%content%" == "base" exit 1  # [win]
+
+  - name: second-{{ name }}
+    script: install.sh  # [unix]
+    script: install.bat  # [win]
+    requirements:
+      host:
+        - {{ pin_subpackage("base-" + name) }}
+      run:
+        - {{ pin_subpackage("base-" + name) }}
+    test:
+      commands:
+        - content="$(cat "${PREFIX}/file")"  # [unix]
+        - test "${content}" = "base"  # [unix]
+        - < "%PREFIX%\file%" set /p content=  # [win]
+        - if not "%content%" == "base" exit 1  # [win]
diff --git a/tests/test_post.py b/tests/test_post.py
index c15fffaf2a..97ef1448fc 100644
--- a/tests/test_post.py
+++ b/tests/test_post.py
@@ -10,7 +10,13 @@
 import pytest
 
 from conda_build import api, post
-from conda_build.utils import get_site_packages, on_win, package_has_file
+from conda_build.utils import (
+    get_site_packages,
+    on_linux,
+    on_mac,
+    on_win,
+    package_has_file,
+)
 
 from .utils import add_mangling, metadata_dir
 
@@ -148,3 +154,19 @@ def test_menuinst_validation_fails_bad_json(testing_config, caplog, tmp_path):
     assert "Found 'Menu/*.json' files but couldn't validate:" not in captured_text
     assert "not a valid menuinst JSON document" in captured_text
     assert "JSONDecodeError" in captured_text
+
+
+@pytest.mark.skipif(on_win, reason="rpath fixup not done on Windows.")
+def test_rpath_symlink(mocker, testing_config):
+    if on_linux:
+        mk_relative = mocker.spy(post, "mk_relative_linux")
+    elif on_mac:
+        mk_relative = mocker.spy(post, "mk_relative_osx")
+    api.build(
+        os.path.join(metadata_dir, "_rpath_symlink"),
+        config=testing_config,
+        variants={"rpaths_patcher": ["patchelf", "LIEF"]},
+        activate=True,
+    )
+    # Should only be called on the actual binary, not its symlinks. (once per variant)
+    assert mk_relative.call_count == 2