fix(stderr): route diagnostics to stderr, keep stdout for data

[AlephNotation]

Problem

vers run --json emits the Warning: vers.toml not found, using default configuration line on stdout, contaminating JSON output and breaking the canonical vers run --json | jq pipeline:

$ vers run --json 2>/dev/null
Warning: vers.toml not found, using default configuration   ← still here, on stdout
{
  "vm_id": "...",
  "head": "..."
}
$ vers run --json | jq .
jq: parse error: Invalid numeric literal at line 1, column 8

Same shape elsewhere — six diagnostics across runconfig, presenters, and handlers were using fmt.Println / fmt.Printf (stdout) instead of stderr.

Fix

Five files, swap fmt.Println → fmt.Fprintln(os.Stderr, …) and fmt.Printf → fmt.Fprintf(os.Stderr, …) for the offending diagnostics:

File	Diagnostic
internal/runconfig/config.go	vers.toml not found warning (the headline bug)
internal/presenters/run_presenter.go	.vers directory not found warning
internal/presenters/branch_presenter.go	no VM IDs returned error + Failed to update HEAD warning
internal/handlers/upgrade.go	skipping checksum verification warning
internal/handlers/kill.go	about to delete VM confirmation header (precedes the interactive prompt)

Verification

$ vers run --json 2>/dev/null
{
  "vm_id": "a46c92a9-36b2-477a-a6f6-694b74945b09",
  "head": "a46c92a9-36b2-477a-a6f6-694b74945b09"
}

$ vers run --json 2>&1 >/dev/null
Warning: vers.toml not found, using default configuration

$ vers run --json | jq .vm_id
"a46c92a9-36b2-477a-a6f6-694b74945b09"

make build, gofmt, go test ./internal/... ./cmd/... all clean.

Addresses agent-native CLI principle 2 (data on stdout, diagnostics on stderr) from the audit. Not a comprehensive sweep — only fixes the cases I happened to see in this session. A broader pass over every fmt.Println / fmt.Printf callsite in internal/ is worth doing as a follow-up.