Execution timer for `shell` tool

### Describe the feature or problem you'd like to solve

Lack of information for how long a shell job has been running

### Proposed solution

The shell tool should give a timer of how many seconds that a command has been running for.

### Example prompts or workflows

Login to a system, check counts for X every 5s for 15s.

### Additional context

This is really useful in scenarios where you want to know how long has it been going for, so that means you know when its hits 15s the work is about to be over rather than a blind wait.

Start by locating the shell tool's execution entry point and tracing how running commands are represented to the user. Determine where elapsed time can be surfaced during a command, then verify the timer against a workflow that checks counts every 5 seconds for 15 seconds. Done means users can see how many seconds the shell job has been running.

Written by the indexing model from the issue text.