Add git_submodules flag to control dependency submodule cloning

[fischeti]

What

Adds a git_submodules option to control whether Bender clones the Git submodules of dependencies.

• Config field git_submodules (default true), mirroring the existing git_lfs option — OR-merged across config layers, validated with unwrap_or(true).
• CLI flag --git-submodules <true|false> (env BENDER_GIT_SUBMODULES), modelled on --git-throttle. It overrides the configured value in either direction.
• When disabled, the git submodule update --init --recursive step is skipped during checkout (along with its per-submodule progress bar).

Why

git submodule update --init --recursive currently runs unconditionally on every checkout that has a .gitmodules file, and it is frequently the slowest part of the initial dependency fetch. In top-level hardware projects, dependency submodules often hold software or tooling that is irrelevant to the build, so cloning them is wasted work. This gives users an escape hatch — persistently via config, or per-invocation via the flag (e.g. in CI).

The default stays true, so existing behavior is unchanged unless explicitly opted out.

Notes

• The flag intentionally takes a value rather than being a presence-only switch (like --no-progress). This keeps the door open to later widening the accepted values — e.g. selecting specific dependencies — without a breaking change to the CLI surface. The config field stays a plain bool for now; no enum is introduced yet.
• Per-dependency / selective submodule control was deliberately not implemented here. The cleaner long-term home for that granularity is producer-side (a dependency declaring which submodule paths it needs), since the consumer generally lacks that knowledge and it doesn't scale to transitive deps.
• Docs updated: book/src/configuration.md (config field reference) and book/src/dependencies.md (Submodules section).

🤖 Generated with Claude Code

[micprog]

I understand the frustration!

From separate conversations, we ideally add a configuration in the Bender.yml indicating which submodules are required, and which are not, on a per-dependency basis, possibly with additional target specification. In this instance, I like the approach to get at least something going. It would be great if we could have a command or option to force the checkout/update of all submodules in all dependencies, just in case we checked out without submodules and now need to get some/all. I think this is a good flag/subcommand for the checkout command, let me know what you think. To avoid breaking setups, I see an option to cleanly get all submodules as a prerequisite to this feature. Other than that, LGTM 👍