I found a typo in the reproduce step. I'm going to fix it here.

The unit test is updated in PR. Now it has some conflicts with the master branch, and I will resolve them soon.

The steps to reproduce the bug:

Assume the file to be debugged is foo.py(You can use any file you want).

1. start pdb: python -m pdb foo.py

2. set a breakpoint on any line of the file:

(Pdb) b 2
Breakpoint 1 at foo.py:2
(Pdb) b
Num Type         Disp Enb   Where
1   breakpoint   keep yes   at foo.py:2

3. when clear the breakpoint using breakpoint number, it will get a output("Deleted breakpoint 1 at ..."):

(Pdb) cl 1
Deleted breakpoint 1 at foo.py:2

4. set another breakpoint:

(Pdb) b 3
Breakpoint 2 at foo.py:3

5. if breakpoint is cleared using (filename:lineno), it gets nothing:

(Pdb)cl foo.py:3
(Pdb)