usages: whole types silently dropped from userDefinedTypes when several files are scanned together (c)

## Summary

`atom usages -l c` silently drops whole entries from `userDefinedTypes` in the emitted
`usages.json`. atom exits `0`, prints no warning, writes well-formed JSON, and lists every scanned
file in `objectSlices` — the types are simply not there.

**Which types go missing changes from run to run over a byte-identical tree.**

Reproduced on **v3.1.1** (current release) and **v3.0.3**, Linux 5.15 (WSL2), x86-64, 8 cores, with
the bundled JDK 23.

## Reproduction

Two files per module: a uniquely-named header with one named struct typedef, and a `.c` that includes
it and uses the type. No build system, no external headers.

```bash
#!/bin/bash
# make-tree.sh [n]
set -eu
root="$1"; n="${2:-10}"; rm -rf "$root"
for i in $(seq 1 "$n"); do
d="$root/mod$i"; mkdir -p "$d"
cat > "$d/Cfg$i.h" < "$d/usa$i.c" <

Start with the `atom usages -l c` entry point and the generated `usages.json`. Rebuild the tree for each run with the supplied `make-tree.sh` reproduction, then compare `userDefinedTypes` with the ten structs expected from the scanned C files. Done means every type is present reliably, with no silent loss when several files are scanned together.

Written by the indexing model from the issue text.