This doesn't fully unbundle it, you also need to use sed to change all
of the

  test_foo_SOURCES += third_party/Catch2-3.14.0/catch_amalgamated_patch.cpp

lines to

  test_foo_LDADD = $(LDADD) -lCatch2 -lCatch2Main

diff --git a/Makefile.am b/Makefile.am
index 8141e769..550a25b4 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -4,7 +4,6 @@
 
 AM_CXXFLAGS =  -I$(abs_top_srcdir)/include
 AM_CXXFLAGS += -I$(abs_top_srcdir)/third_party # for backward-cpp
-AM_CXXFLAGS += -I$(abs_top_srcdir)/third_party/Catch2-3.14.0
 AM_CXXFLAGS += -I$(abs_top_srcdir)/third_party/HPCombi-1.1.2/include
 AM_CXXFLAGS += -I$(abs_top_srcdir)/third_party/HPCombi-1.1.2/third_party
 AM_CXXFLAGS += -I$(abs_top_srcdir)/third_party/rx-ranges/include
@@ -216,9 +215,6 @@ detailinclude_HEADERS += include/libsemigroups/detail/word-graph-with-sources.hp
 detailinclude_HEADERS += include/libsemigroups/detail/word-graph-with-sources.tpp
 detailinclude_HEADERS += include/libsemigroups/detail/word-iterators.hpp
 
-catch2includedir = $(includedir)/libsemigroups/Catch2-3.14.0/
-catch2include_HEADERS = third_party/Catch2-3.14.0/catch_amalgamated.hpp
-
 if USE_BUNDLED_MAGIC_ENUM
 magicenumincludedir = $(includedir)/libsemigroups/magic_enum
 magicenuminclude_HEADERS = third_party/magic_enum-0.9.7/include/magic_enum/magic_enum.hpp
@@ -1128,8 +1124,6 @@ EXTRA_DIST += hpcombi.mk.in
 EXTRA_DIST += tests/bmat-data.hpp
 EXTRA_DIST += tests/test-main.hpp
 EXTRA_DIST += tests/word-graph-test-common.hpp
-EXTRA_DIST += third_party/Catch2-3.14.0/catch_amalgamated.cpp
-EXTRA_DIST += third_party/Catch2-3.14.0/catch_amalgamated.hpp
 EXTRA_DIST += third_party/HPCombi-1.1.2/HPCOMBI_VERSION
 EXTRA_DIST += third_party/HPCombi-1.1.2/LICENSE
 EXTRA_DIST += third_party/HPCombi-1.1.2/README.md