fix(cli/pack): excluded entries nested within included dirs

[DonIsaac]

What does this PR do?

Fixes #18505

Other changes:

• Pack Pattern's boolean fields into a packed Flags struct

How did you verify your code works?

I have added a test

[robobun]

^{Updated 7:26 PM PT - Mar 28th, 2025}

❌ @DonIsaac, your commit 1d5c89c has 1 failures in Build #14213:

• test/cli/create/create-jsx.test.ts - 2 failing on 🍎 14 aarch64
• test/cli/create/create-jsx.test.ts - 2 failing on 🍎 13 aarch64
• test/cli/create/create-jsx.test.ts - 2 failing on 🍎 14 x64
• test/cli/create/create-jsx.test.ts - 2 failing on 🍎 13 x64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 3.21 aarch64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 3.21 x64-baseline
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 3.21 x64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 12 aarch64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 22.04 aarch64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 24.04 aarch64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 20.04 aarch64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 12 x64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 22.04 x64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 12 x64-baseline
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 20.04 x64-baseline
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 22.04 x64-baseline
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 24.04 x64
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 24.04 x64-baseline
• test/cli/create/create-jsx.test.ts - 2 failing on 🐧 20.04 x64

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🧪   try this PR locally:

bunx bun-pr 18509

[dylan-conway]

After LICENSE comment is addressed this looks good to go