FileSystemDirectoryReader.readEntries() only returns 100 entries a time, must be called repeatedly to enumerate all entries.

enumerate-dir-with-more-than-100-files.js

function readEntriesAsync(reader) {
    return new Promise((resolve, reject) => {
        reader.readEntries(entries => {
            resolve(entries);
        }, error => reject(error));
    })
}

async function enumerateDirectoryWithManyFiles(directoryEntry) {
    let reader = directoryEntry.createReader();
    let resultEntries = [];

    let read = async function() {
        let entries = await readEntriesAsync(reader);
        if (entries.length > 0) {
            resultEntries = resultEntries.concat(entries);
            await read();
        }
    }

    await read();
    return resultEntries;
}

// Run in chrome extension's background page's console
chrome.runtime.getPackageDirectoryEntry(async rootEntry => {
    let entries = await enumerateDirectoryWithManyFiles(rootEntry);
    console.log(entries);
})