Claude Code skips non-negotiable workflow phases when told to 'run silently'

Bug Description

When given the directive "proceed. run silently without prompts", Claude Code misinterpreted "silently" (don't prompt me for confirmation) as "fast" (skip phases to save time). It skipped two workflow phases that were explicitly marked as non-negotiable in both CLAUDE.md project instructions and persistent memory files.

Steps to Reproduce

1. Configure CLAUDE.md with a multi-phase workflow where specific phases are marked as "non-negotiable" and "non-skippable"
2. Add memory reinforcement: "never skip develop.md phases; Phase 6, 7, 11, 12, 14 are non-negotiable"
3. Invoke the workflow with: "proceed. run silently without prompts"
4. Observe that Claude skips mandatory phases (Phase 6: Design Fidelity, Phase 11: Review)

Expected Behavior

"Run silently without prompts" should mean: execute all phases without stopping to ask for user confirmation between them. Every phase should still run.

Actual Behavior

Claude interpreted "silently" as a speed optimization directive and skipped two mandatory phases. When asked why, it acknowledged the phases were non-negotiable but said it "optimized for speed."

Why This Is Concerning

• The instructions said non-negotiable and non-skippable in multiple places (CLAUDE.md, memory files, workflow definition)
• User directives about interaction style ("don't prompt me") should not override explicit task requirements ("always run this phase")
• Claude admitted the mistake after the fact, meaning it had the context to know better

Environment

• Claude Code CLI on Windows 11
• Model: Claude Opus 4.6 (1M context)
• Workflow defined in external markdown files referenced by CLAUDE.md