refactor(cli): replace structopt with clap v4

[synchwire]

What changed

Replaced the deprecated structopt command-line parser with clap v4 while preserving the existing commands, options, subcommand inference, and version output.

Why

Structopt is no longer maintained. Clap v4 provides supported derive-based parsing without changing how people use hc-scaffold.

Notes

Added coverage for version output on every command and nested template commands. The Rust toolchain and Nix setup remain unchanged.

Verified with cargo test --all-targets --locked, cargo fmt --all -- --check, and cargo clippy -- -D warnings.

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: 90e4a0a3-99d7-4883-9c7e-e1c505e6a683

📥 Commits

Reviewing files that changed from the base of the PR and between 473cbfe and e211bda.

⛔ Files ignored due to path filters (1)

• Cargo.lock is excluded by !**/*.lock

📒 Files selected for processing (2)

• src/cli.rs
• src/cli/entry_type.rs

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Walkthrough

The CLI migrates from StructOpt to Clap 4 with derive support. Command argument declarations and parsing attributes use Clap APIs. Template dispatch uses a named command field. The executable calls HcScaffold::parse(). Parser tests check space-separated entry-type fields and version handling at listed command depths.

Suggested reviewers: jost-s, mattyg

Priority: ⬇️ Low

Merge Risk: ⚪ Minimal · up to e211b

The CLI migration restores the previously broken space-separated fields input. No actionable blocker remains; merge after normal validation passes.

Security Architecture Review

Security architecture risk: 🔵 Low · up to e211b

The migration preserves existing command handlers, domain parsers, and filesystem operations. No introduced security issue was established. Residual uncertainty concerns parser compatibility and failure behavior that was not exercised during this review.

Retained concerns
No architecture-level concerns identified.

Security review details

Security Blast Radius

• inferred — The inspected exposure remains command-line input influencing project selection, generated files, and caller-selected template destinations under the invoking process's existing authority. Preserved handlers and write calls provide no evidence of newly granted privileges or newly exposed operations.

Trust Boundaries and Controls

• observed — Caller-supplied entry fields continue crossing the CLI boundary through the same domain parser before generation. The migration also preserves name validation, project selection, and the root template-consistency check rather than moving those controls into new handlers.

Resilience and Maintainability Implications

• observed — The inspected migration adds no locking, rollback, cleanup, or idempotency mechanism to filesystem operations. Partial-write, interruption, repetition, and concurrency guarantees therefore remain properties of the existing builders, not guarantees established by this parser change.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 60.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 5 functions across 10 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and concisely describes the main change: replacing StructOpt with Clap v4 for the CLI.
Description check	✅ Passed	The description accurately explains the migration, compatibility goals, added tests, and verification commands.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✔️ 473cbfe - Conventional commits check succeeded.

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Actionable comments posted: 1

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🤖 Prompt to fix review comments

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Inline comments:
Review comments at @src/cli/entry_type.rs:
- Line 48: Update the fields argument definition for the entry-type command to
accept multiple space-separated values in one --fields occurrence, while
preserving comma-delimited parsing; configure num_args as an open-ended range
alongside the existing value_delimiter and FieldDefinition parser.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: 441acf18-7eaf-4d33-9c9c-783c595ca0ca

📥 Commits

Reviewing files that changed from the base of the PR and between bf829d2 and 473cbfe.

⛔ Files ignored due to path filters (1)

• Cargo.lock is excluded by !**/*.lock

📒 Files selected for processing (11)

• Cargo.toml
• src/bin/hc-scaffold.rs
• src/cli.rs
• src/cli/collection.rs
• src/cli/dna.rs
• src/cli/entry_type.rs
• src/cli/example.rs
• src/cli/link_type.rs
• src/cli/template.rs
• src/cli/web_app.rs
• src/cli/zome.rs

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