#40062 test: update bun-pm.test.ts `pm ls` snapshots for #38952's header; name prune's HoistedTree::init flags

What does this PR do?

Two small fixes for things currently red on main for any PR that touches bun_install:

1. test/cli/install/bun-pm.test.ts — #39962 added three bun pm ls inline snapshots using the old node_modules (N) header, and #38952 (merged around the same time) changed that header to node_modules (N installed). The two crossed, so those three snapshots fail on main. Updated them to the current wording. Same for one bun-prune.test.ts --verbose snapshot that predates #38952's checked N installed packages wording.
2. src/install/prune.rs — the mordant bare_bool_args lint flags HoistedTree::init(before, true, false) (0 recorded in the baseline for that file), which fails the rust-lints / mordant job on PRs touching the crate (seen on #40011 and #40053, neither of which touches prune.rs). init now takes a small named options struct.

No behaviour change.

How did you verify your code works?

bun test test/cli/install/bun-pm.test.ts passes locally (was 3 failures on main); cargo clippy -p bun_install clean; bun-prune.test.ts unchanged.