deno run on a symlinked entry resolves relative imports against the symlink, not its realpath #35545

Version: Deno 2.9.0

deno 2.9.0 (stable, release, x86_64-unknown-linux-gnu)
v8 14.9.207.2-rusty
typescript 6.0.3

Linux. Worked on an earlier 2.x — looks like a recent regression, not bisected.

Bug

When the entry module given to deno run is a symlink, Deno uses the symlink's path as the main-module URL and resolves the module's relative imports from the symlink's directory — instead of realpath-ing the entry first.

This breaks node_modules/.bin/<tool> shims (symlinks into a package's bin/), whose scripts import siblings like ../src/…. Node and Bun resolve the symlink first; Deno 2.9.0 resolves one level wrong and fails with Module not found.

Repro

mkdir -p repro/pkg/bin repro/pkg/lib repro/.bin && cd repro
printf '%s\n' '#!/usr/bin/env -S deno run --allow-all' "import {x} from '../lib/x.js';" 'console.log(x);' > pkg/bin/cli.js
echo "export const x = 'ok';" > pkg/lib/x.js
ln -s ../pkg/bin/cli.js .bin/cli        # as npm creates under node_modules/.bin

deno run --allow-all .bin/cli           # symlink   -> error
deno run --allow-all pkg/bin/cli.js     # real path -> ok

Actual

$ deno run --allow-all .bin/cli
error: Module not found "file:///…/repro/lib/x.js".
    at file:///…/repro/.bin/cli:2:17

The main module is …/.bin/cli (the symlink), so ../lib/x.js resolves to repro/lib/x.js (missing) instead of repro/pkg/lib/x.js (the target's sibling). Run via the real path it prints ok.

Expected

deno run <symlink> realpaths the entry before resolving relative imports — matching Node and Bun — so both invocations print ok.