fix(molecule): use Dependencies from bd show instead of empty DependsOn (#901)

* fix(molecule): use Dependencies from bd show instead of empty DependsOn

Bug: Molecule step dependency checking was broken because bd list
doesn't populate the DependsOn field (it's always empty). Only bd show
returns dependency info in the Dependencies field.

This caused all open steps to appear "ready" regardless of actual
dependencies - the polecat would start blocked steps prematurely.

Fix: Call ShowMultiple() after List() to fetch full issue details
including Dependencies, then check Dependencies instead of DependsOn.

Affected functions:
- findNextReadyStep() in molecule_step.go
- getMoleculeProgressInfo() in molecule_status.go
- runMoleculeCurrent() in molecule_status.go

Tests:
- Added TestFindNextReadyStepWithBdListBehavior to verify fix
- Added TestOldBuggyBehavior to demonstrate the bug
- Updated existing tests to use fixed algorithm

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* fix(molecule): use Dependencies from bd show instead of empty DependsOn

Bug: Molecule step dependency checking was broken because bd list
doesn't populate the DependsOn field (it's always empty). Only bd show
returns dependency info in the Dependencies field.

This caused all open steps to appear "ready" regardless of actual
dependencies - the polecat would start blocked steps prematurely.

Fix: Call ShowMultiple() after List() to fetch full issue details
including Dependencies, then check Dependencies instead of DependsOn.
Also filter to only check "blocks" type dependencies - ignore "parent-child"
relationships which are just structural, not blocking.

Affected functions:
- findNextReadyStep() in molecule_step.go
- getMoleculeProgressInfo() in molecule_status.go
- runMoleculeCurrent() in molecule_status.go

Tests:
- Added TestFindNextReadyStepWithBdListBehavior to verify fix
- Added TestOldBuggyBehavior to demonstrate the bug
- Updated existing tests to use fixed algorithm

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

---------

Co-authored-by: julianknutsen <julianknutsen@users.noreply.github>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

internal/cmd/molecule_step.go

@@ -205,11 +205,11 @@ func findNextReadyStep(b *beads.Beads, moleculeID string) (*beads.Issue, bool, e
 		return nil, true, nil // No steps = complete
 	}
 
-	// Build set of closed step IDs and collect open steps
+	// Build set of closed step IDs and collect open step IDs
 	// Note: "open" means not started. "in_progress" means someone's working on it.
 	// We only consider "open" steps as candidates for the next step.
 	closedIDs := make(map[string]bool)
-	var openSteps []*beads.Issue
+	var openStepIDs []string
 	hasNonClosedSteps := false
 
 	for _, child := range children {
@@ -217,7 +217,7 @@ func findNextReadyStep(b *beads.Beads, moleculeID string) (*beads.Issue, bool, e
 		case "closed":
 			closedIDs[child.ID] = true
 		case "open":
-			openSteps = append(openSteps, child)
+			openStepIDs = append(openStepIDs, child.ID)
 			hasNonClosedSteps = true
 		default:
 			// in_progress or other status - not closed, not available
@@ -230,17 +230,42 @@ func findNextReadyStep(b *beads.Beads, moleculeID string) (*beads.Issue, bool, e
 		return nil, true, nil
 	}
 
+	// No open steps to check
+	if len(openStepIDs) == 0 {
+		return nil, false, nil
+	}
+
+	// Fetch full details for open steps to get dependency info.
+	// bd list doesn't return dependencies, but bd show does.
+	openStepsMap, err := b.ShowMultiple(openStepIDs)
+	if err != nil {
+		return nil, false, fmt.Errorf("fetching step details: %w", err)
+	}
+
 	// Find ready steps (open steps with all dependencies closed)
-	for _, step := range openSteps {
+	for _, stepID := range openStepIDs {
+		step, ok := openStepsMap[stepID]
+		if !ok {
+			continue
+		}
+
+		// Check dependencies using the Dependencies field (from bd show),
+		// not DependsOn (which is empty from bd list).
+		// Only "blocks" type dependencies block progress - ignore "parent-child".
 		allDepsClosed := true
-		for _, depID := range step.DependsOn {
-			if !closedIDs[depID] {
+		hasBlockingDeps := false
+		for _, dep := range step.Dependencies {
+			if dep.DependencyType != "blocks" {
+				continue // Skip parent-child and other non-blocking relationships
+			}
+			hasBlockingDeps = true
+			if !closedIDs[dep.ID] {
 				allDepsClosed = false
 				break
 			}
 		}
 
-		if len(step.DependsOn) == 0 || allDepsClosed {
+		if !hasBlockingDeps || allDepsClosed {
 			return step, false, nil
 		}
 	}