fix: propagate Connect/PM command/args overrides through Site CR

[ssinnott]

Description

#156 added optional Command []string / Args []string fields to ConnectSpec and PackageManagerSpec so the hardcoded tini-wrapper entrypoint (tini -- /usr/local/bin/startup.sh) can be overridden or dropped. It only touched the standalone Connect/PackageManager CRDs, though — the Site CR's embedded InternalConnectSpec/InternalPackageManagerSpec types (api/core/v1beta1/site_types.go) have no equivalent fields, so anything deployed via a Site (which is how most consumers, including Posit's own agave environment, actually run these products) has no way to set them.

This follows up #156 for the Site path: adds Command/Args to both Internal*Spec types and threads them through SiteReconciler.reconcileConnect/reconcilePackageManager into the child Connect/PackageManager CRs it manages, using the exact same field docs/semantics as #156 (unset on both falls back to the legacy tini wrapper via resolveEntrypoint — no default behavior change for existing Sites).

Motivation

posit-dev/images-connect-built images (the daily/preview channel) don't ship tini, so any Site tracking that channel crash-loops on exec: "tini": executable file not found in $PATH with no way to work around it short of this fix.

Code Flow

• InternalConnectSpec.Command/.Args and InternalPackageManagerSpec.Command/.Args added (api/core/v1beta1/site_types.go).
• site_controller_connect.go / site_controller_package_manager.go: pass site.Spec.Connect.Command/Args and site.Spec.PackageManager.Command/Args straight through to the child CR's spec, mirroring every other pass-through field in those functions.
• Regenerated: zz_generated.deepcopy.go, client-go/applyconfiguration/..., config/crd/bases/core.posit.team_sites.yaml, dist/chart/templates/crd/core.posit.team_sites.yaml, internal/crdapply/bases/core.posit.team_sites.yaml (via make generate-all manifests copy-crds helm-generate).

Category of change

• Breaking change

Purely additive — nil Command/Args on a Site's connect/packageManager spec continues to fall back to the legacy tini wrapper exactly as before.

Checklist

• I have run just test and all tests pass
• I have reviewed my own diff and added inline comments on lines I want reviewers to focus on or that I am uncertain about

Testing

Added 4 reconciler tests mirroring #156's pattern: TestSiteReconciler_ConnectCommandArgsPropagation/DefaultNil and TestSiteReconciler_PackageManagerCommandArgsPropagation/DefaultNil, covering both the explicit-override and default (nil, legacy-wrapper-preserving) cases for each product.

[claude]

Claude finished @ssinnott's task in 1m 18s —— View job

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Code Review

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The implementation is correct and follows existing patterns well. The propagation is a straight pass-through, the deep copy and generated code are consistent, and the tests cover both the propagation and the nil-default cases.

One observation and one minor note:

InternalConnectSpec / InternalPackageManagerSpec are missing Sleep

The standalone ConnectSpec and PackageManagerSpec both have a Sleep bool field that overrides Command/Args with "sleep infinity" (connect_types.go:121, packagemanager_types.go:77). InternalConnectSpec and InternalPackageManagerSpec don't expose it, so Site users have never been able to use it — that's a pre-existing gap, not introduced here. Worth noting in case a follow-up adds Sleep support to Site later; the Command/Args plumbing this PR adds is the right prerequisite.

// +optional is redundant for []string with omitempty (api/core/v1beta1/site_types.go:234,240,325,331)

The +optional marker is only meaningful when a field lacks omitempty (it tells controller-gen the field is not required). Since all four new fields already have omitempty, the annotation is a no-op. This matches how the standalone ConnectSpec/PackageManagerSpec annotate the same fields, so it's consistent — but it's cargo-culted boilerplate. Fine to leave as-is for consistency; mentioning it for awareness.

Everything else looks good:

• Deep copy is correct (make + copy for each slice).
• Apply-configuration methods match the generated pattern used elsewhere.
• CRD YAML in all three locations (config/, dist/chart/, internal/crdapply/) is in sync.
• Tests are clear and cover both the explicit-override and nil-default paths for each product.

[Copilot]

Pull request overview

This PR extends the Site CRD’s embedded Connect and Package Manager specs to support command/args overrides, and propagates those fields into the child Connect / PackageManager CRs created by the SiteReconciler, aligning the Site-based deployment path with the standalone product CRDs.

Changes:

• Added Command []string / Args []string to InternalConnectSpec and InternalPackageManagerSpec (Site API types) with matching CRD schema regeneration.
• Threaded site.Spec.Connect.Command/Args and site.Spec.PackageManager.Command/Args through the Site reconciler into the child CR specs.
• Added reconciler tests to validate propagation and default-nil behavior.

Reviewed changes

Copilot reviewed 6 out of 10 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
api/core/v1beta1/site_types.go	Adds Command/Args to Site’s internal Connect/PM specs.
api/core/v1beta1/zz_generated.deepcopy.go	Regenerated deep-copies for the new slice fields.
internal/controller/core/site_controller_connect.go	Propagates Site Connect Command/Args into the child Connect CR.
internal/controller/core/site_controller_package_manager.go	Propagates Site Package Manager Command/Args into the child PackageManager CR.
internal/controller/core/site_test.go	Adds tests for propagation and default-nil behavior for both products.
client-go/applyconfiguration/core/v1beta1/internalconnectspec.go	Regenerates applyconfiguration for Site internal Connect spec with new fields.
client-go/applyconfiguration/core/v1beta1/internalpackagemanagerspec.go	Regenerates applyconfiguration for Site internal PM spec with new fields.
config/crd/bases/core.posit.team_sites.yaml	Regenerates Site CRD base schema to expose command/args.
dist/chart/templates/crd/core.posit.team_sites.yaml	Regenerates Helm-rendered Site CRD with command/args.
internal/crdapply/bases/core.posit.team_sites.yaml	Regenerates internal CRD-apply base with command/args.

Files not reviewed (3)

• api/core/v1beta1/zz_generated.deepcopy.go: Generated file
• client-go/applyconfiguration/core/v1beta1/internalconnectspec.go: Generated file
• client-go/applyconfiguration/core/v1beta1/internalpackagemanagerspec.go: Generated file

Suppressed comments (2)

client-go/applyconfiguration/core/v1beta1/internalpackagemanagerspec.go:151

• Comment typo: use "objects can be built" (past participle) for grammatical correctness and consistency with other applyconfiguration comments.
  client-go/applyconfiguration/core/v1beta1/internalconnectspec.go:181
• Comment typo: use "objects can be built" (past participle) for grammatical correctness and consistency with other applyconfiguration comments.

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[Lytol]

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