Tool files are copied without execute bit

Some tools rely on tool files being executable, but when Pulsar transfers them, they are written without the execute bit set, and the tool fails. For example, ` toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.0 `:

```console
% ls -l /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/37e1eb05b1b4/text_processing/ansi2html.sh
-rwxr-xr-x. 1 g2main G-803372 11886 Mar 1 2016 /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/37e1eb05b1b4/text_processing/ansi2html.sh*
% ls -l /jetstream2/scratch/main/jobs/53425066/tool_files/ansi2html.sh
-rw-r--r-- 1 g2main G-803372 11886 Nov 3 00:44 /jetstream2/scratch/main/jobs/53425066/tool_files/ansi2html.sh
```

Which results in the error:

```
/jetstream2/scratch/main/jobs/53425066/tool_script.sh: line 23: /jetstream2/scratch/main/jobs/53425066/tool_files/ansi2html.sh: Permission denied
```

Trace how tool files are transferred from the toolshed path into the job's tool_files directory, using ansi2html.sh and the tool_script.sh error as the example. Compare the source and destination permissions, then verify that transferred executable tools can run without the Permission denied failure.

Written by the indexing model from the issue text.