fix(cli): preserve directory basename for filtered uploads

[johntmyers]

Summary

Make named directory uploads preserve the source directory basename consistently, including the default git-filtered upload path. .gitignore filtering now only decides which files are included; it no longer changes where those files land in the sandbox.

Related Issue

Fixes #885

Changes

• Reused one archive writer for single-path and git-filtered upload archives.
• Added an optional archive prefix for git-filtered file lists so named directories land under <dest>/<basename>/....
• Kept flat archive layout for upload . and file uploads.
• Documented that filtering affects inclusion, not destination layout.

Testing

• mise run pre-commit passes
• Unit tests added/updated
• E2E tests added/updated (if applicable)

Checklist

• Follows Conventional Commits
• Commits are signed off (DCO)
• Architecture docs updated (if applicable)

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[mjamiv]

Sorry for the noise on #976. My follow-up commit for the repo-backed/git-filtered path landed on my flag branch, not the PR branch John was reviewing. Thanks for carrying the #885 fix forward here.

I fetched this PR locally at cc51dff and ran the focused upload coverage:

• cargo test -p openshell-cli archive — 4 passed
• cargo test -p openshell-cli directory_upload_prefix — 2 passed

The behavior here matches the #885 production footgun we hit: named directory uploads preserve <dest>/<basename>/..., while upload . / basename-less paths keep the legacy flat behavior. The current Rust CI failure looks unrelated to this diff; it is in openshell-sandbox process identity ambiguity handling.