fix build failure with gcc 13

[emollier]

As seen initially in Debian bug#1037662, per gcc 13 porting guide, there have been header dependency changes resulting in the following build errors:

In file included from repeat_graph/repeat_graph.h:10,
                 from repeat_graph/graph_processing.h:10,
                 from repeat_graph/graph_processing.cpp:7:
repeat_graph/../sequence/sequence_container.h:21:37: error: expected ‘)’ before ‘id’
   21 |                 explicit Id(uint32_t id): _id(id) {}
      |                            ~        ^~~
      |                                     )
repeat_graph/../sequence/sequence_container.h:69:17: error: ‘uint32_t’ does not name a type
   69 |                 uint32_t _id;
      |                 ^~~~~~~~
repeat_graph/../sequence/sequence_container.h:13:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?

[…]

In file included from polishing/alignment.h:14,
                 from polishing/alignment.cpp:5:
polishing/subs_matrix.h:47:34: error: ‘uint32_t’ has not been declared
   47 |                 State(char nucl, uint32_t length);
      |                                  ^~~~~~~~
polishing/subs_matrix.h:53:17: error: ‘uint32_t’ does not name a type
   53 |                 uint32_t length;
      |                 ^~~~~~~~
polishing/subs_matrix.h:13:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?

Including cstdint in the affect header files fixes the issue.

[fenderglass]

Thank you, merged!