Granular tool permission controls — allow-list specific tools

## Description:

Currently, Tool permissions only offers two options: "Approve all" or "Ask every time". There is no way to allow specific tools automatically while still requiring approval for others.

## Requested feature:

Add per-tool permission configuration in Settings → Sessions → Tool permissions, allowing users to define an allow-list of tools that run without confirmation (e.g. grep, glob, view) while all other tools still require explicit approval.

## Use case:

Read-only tools like grep/ripgrep pose no risk to the codebase and interrupting the agent flow to approve every search is disruptive. Write/execute tools (bash, file edit, git push) should still require confirmation. A middle ground between "trust everything" and "approve everything" would significantly improve agent UX without sacrificing safety on destructive operations.

## Proposed UI:

In the Tool permissions dropdown, add a third option: "Custom" — opens a list of available tools with individual allow/ask toggles per tool.

Start in Settings → Sessions → Tool permissions and trace how the existing “Approve all” and “Ask every time” choices are represented and applied. Done means a “Custom” option provides per-tool allow/ask toggles, with allow-listed tools skipping confirmation while all others still prompt, including the read-only and write/execute examples.

Written by the indexing model from the issue text.