Clean up dead code suppressed with #[allow(dead_code)]

[astefano]

Context

In commit 1eb0832, we added #![allow(dead_code)] to five modules to pass cargo clippy -D warnings in CI. These modules contain code that is not yet wired into the CLI's command dispatch.

Files with #![allow(dead_code)]

File	Contents	Reason
src/commands/api.rs	.verilib file CRUD (get/set/list/batch)	API subcommand not exposed in cli.rs
src/commands/deploy.rs	Repository deployment flow	Deploy command not exposed in cli.rs
src/commands/types.rs	DeployNode, DeployResponse, DeployData structs	Used only by deploy.rs
src/download/client.rs	download_repo, wait_for_atomization	Download/pull flow not exposed
src/download/types.rs	TreeNode, Snippet, DownloadResponse, etc.	Used only by download/client.rs

Action items

For each file, decide one of:

1. Wire it in: expose the command in cli.rs and main.rs, remove the suppression
2. Remove it: if the code is obsolete or superseded, delete the file and remove the mod declaration
3. Keep suppressed: if it's actively being developed but not ready yet, leave as-is

Once all files are resolved, this issue can be closed.