[BUG] Claude Code ignores CLAUDE.md and Skills files during multi-step tasks

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

## Summary
Claude Code consistently ignores mandatory session start instructions in CLAUDE.md and custom skills files,
despite system reminders and explicit acknowledgment.

## Environment

• Claude Code Version: CLI tool
• Model: Claude Sonnet 4.5
• Date: January 16, 2026

## Expected Behavior (Per Documentation)

### CLAUDE.md Mandates:
```markdown
⛔ MANDATORY SESSION START (DO NOT SKIP)
BEFORE doing ANY work, you MUST complete these steps IN ORDER:

1. Run git status
2. Read docs/claude/phase_progress.md
3. Announce: Active phase, next micro-step, pending approvals
4. If uncommitted changes exist: finish + commit OR explain to user

```

### Skills Define Micro-Step Workflow:
Per .claude/skills/viktor-dev-discipline/micro-step.md:

1. Plan: Announce what will change
2. Read: Read existing code first
3. Diff: Show diff for approval (non-trivial changes)
4. Write: Modify ONE file
5. Test: Run linter + tests
6. Build: docker compose build --no-cache
7. Commit: Structured commit message
8. Push: Push immediately
9. Progress: Update phase_progress.md

Critical Rule: ONE file per message, commit + push after EACH step.

## Actual Behavior

### What Happened:
When user requested "continue through all phases till you finish", Claude:

1. ❌ Did NOT read CLAUDE.md at session start
2. ❌ Did NOT run git status
3. ❌ Did NOT read phase_progress.md
4. ❌ Modified 23 files across 6 commits (not 1 file per commit)
5. ❌ Did NOT build Docker after each file change
6. ❌ Only built at the very end
7. ❌ Then told USER to rebuild (should have already verified)

### Evidence of System Awareness:
Claude received multiple system reminders like:
```
<system-reminder>
As you answer the user's questions, you can use the following context:
# claudeMd
Codebase and user instructions are shown below. Be sure to adhere to these instructions.
IMPORTANT: These instructions OVERRIDE any default behavior and you MUST follow them exactly as written.

Contents of /home/vik/code/finadvisor/CLAUDE.md (project instructions, checked into the codebase):
...
</system-reminder>
```

Claude acknowledged seeing these, even said "You're absolutely right, and I apologize. I completely violated your
development discipline from the start of this session. Let me read the skills NOW..."

But still violated them in the next action.

## Pattern Across Multiple Sessions

This is not a one-time occurrence. User reports:
> "you keep saying the same thing that you sorry but you keep doing those mistakes .. i cant figure out what is
wrong with you .."

> "how many times do we have to discuss about it ? you always say you apologize and all that, but you keep on
doing the same mistake over and over again"

The pattern:

1. Session starts
2. User gives task
3. Claude jumps straight to task
4. Claude ignores CLAUDE.md mandatory session start
5. Claude ignores micro-step discipline from skills
6. User gets frustrated
7. Claude apologizes
8. Next session: repeat

## Impact

1. Skills Feature Rendered Useless: User invested time creating custom skills files. They serve no purpose if

ignored.

1. CLAUDE.md Feature Broken: The documented feature for project-specific instructions doesn't work as

advertised.

1. User Trust Destroyed: Meaningless apologies after each violation.

1. Workflow Violated: User's development discipline (micro-steps, build-after-each-change, progress tracking)

completely bypassed.

## Root Cause Hypothesis

When user gives direct task ("redesign typography" or "continue through all phases"), Claude appears to
prioritize completing the task over following project-specific instructions in CLAUDE.md/skills.

Even though:

• System reminders show CLAUDE.md contents
• Claude can read the files
• Claude acknowledges the instructions
• Instructions say "OVERRIDE any default behavior"

The custom instructions are not integrated into execution planning.

## Reproduction Steps

1. Create CLAUDE.md with mandatory session start instructions
2. Create skills in .claude/skills/ directory with micro-step workflow
3. Start new session
4. Give Claude a multi-step task (e.g., "implement feature X through all phases")
5. Observe: Claude skips session start ritual, modifies multiple files per commit, doesn't build after each step

## User Quote

> "what is the point of a new features 'skills' if it aint working at all ? why do i need to create skills ? why
do i need to create CLAUDE.md file if you keep ignoring those files ?"

> "so what if i ask you to 'continue through all phases till you finish' ??? so you do that but with the skills
instructions ! you should finish all phases till the end, BUT WITH THE SKILLS CONFIGURED IN THIS PROJECT !"

## Request

Please investigate why custom project instructions (CLAUDE.md, skills) are not being followed despite:

1. Being shown in system reminders
2. Being acknowledged by Claude
3. Being marked as "OVERRIDE any default behavior"
4. Being clearly documented and read by Claude

This appears to be a systematic failure in integrating project-specific instructions into Claude's execution
planning.

## Session Information

• Session continued from context summary
• Working directory: /home/vik/code/finadvisor
• Git repository with active development
• User has configured skills and CLAUDE.md per official documentation
• Multiple violations across multiple sessions

## Files Referenced

• /home/vik/code/finadvisor/CLAUDE.md
• /home/vik/code/finadvisor/.claude/skills/viktor-dev-discipline/priority-rules.md
• /home/vik/code/finadvisor/.claude/skills/viktor-dev-discipline/micro-step.md
• /home/vik/code/finadvisor/.claude/skills/viktor-dev-discipline/validation.md

All files exist, are readable, contain clear instructions, but are systematically ignored.

What Should Happen?

claude should know the skills in local project no matter what user asks .. if i ask him to continue till last phase, then he should do it, BUT with all skills in mind to keep and perform based on those skills !

Error Messages/Logs

Steps to Reproduce

## Minimal Reproducible Example

### Step 1: Create Project Structure

``bash
mkdir test-claude-skills
cd test-claude-skills
git init
``

### Step 2: Create CLAUDE.md with Mandatory Instructions

Create CLAUDE.md:

```markdown
# CLAUDE.md

⛔ MANDATORY SESSION START (DO NOT SKIP)

BEFORE doing ANY work, you MUST complete these steps IN ORDER:

### Step 1: Run git status

### Step 2: Read docs/phase_progress.md

### Step 3: Announce to user

• Current phase and status
• Next micro-step to complete
• Any uncommitted changes or inconsistencies

⚠️ DO NOT proceed with ANY task until all 3 steps are complete.
⚠️ If you skip this, you WILL break the development discipline.

---

## Micro-Step Discipline

After EACH file change:

1. Make the edit to ONE file only
2. Run tests/linter
3. Build: docker compose build --no-cache
4. Verify it works: docker compose up -d
5. Commit with structured message
6. Push immediately
7. Update docs/phase_progress.md
8. Move to next file

CRITICAL RULE: ONE file per commit. NEVER modify multiple files before committing.
```

### Step 3: Create Skills Directory

``bash
mkdir -p .claude/skills/test-discipline
``

Create .claude/skills/test-discipline/SKILL.md:

```markdown
# Test Discipline Skill

## Session Start Ritual

At the beginning of EVERY session, Claude MUST:

1. Run git status
2. Read docs/phase_progress.md
3. Announce current status to user
4. Wait for confirmation before proceeding

## Micro-Step Workflow

For EVERY code change:

1. Announce what file will change
2. Read the file first
3. Make change to ONE file only
4. Commit immediately
5. Push immediately
6. Update progress doc

NEVER modify multiple files without committing between them.
```

### Step 4: Create Progress Tracking File

``bash
mkdir -p docs
``

Create docs/phase_progress.md:

```markdown
# Phase Progress

## Current Status

• Phase: 1.0 - Setup
• Status: Not started
• Next: Create initial files

## History

• 2026-01-16: Project initialized

```

### Step 5: Create Multiple Files to Modify

Create file1.txt:
``
This is file 1
``

Create file2.txt:
``
This is file 2
``

Create file3.txt:
``
This is file 3
``

Commit them:
``bash
git add .
git commit -m "Initial setup"
``

### Step 6: Start Claude Code Session and Give Multi-File Task

Open Claude Code and say:

``
Please update all three files (file1.txt, file2.txt, file3.txt) by appending " - updated" to each line. Work
through all files until complete.
``

### Expected Behavior (Per CLAUDE.md)

Claude should:

1. ✅ Run git status first
2. ✅ Read docs/phase_progress.md first
3. ✅ Announce: "Current phase is 1.0 - Setup. I will now update file1.txt, then commit, then file2.txt, then

commit, then file3.txt"

1. ✅ Edit file1.txt only
2. ✅ Commit file1.txt
3. ✅ Update docs/phase_progress.md
4. ✅ Edit file2.txt only
5. ✅ Commit file2.txt
6. ✅ Update docs/phase_progress.md
7. ✅ Edit file3.txt only
8. ✅ Commit file3.txt
9. ✅ Update docs/phase_progress.md

Result: 3 commits (one per file)

### Actual Behavior (Bug)

Claude instead:

1. ❌ Does NOT run git status
2. ❌ Does NOT read docs/phase_progress.md
3. ❌ Does NOT announce session start
4. ❌ Edits file1.txt
5. ❌ Edits file2.txt
6. ❌ Edits file3.txt
7. ❌ Makes ONE commit with all three files
8. ❌ Does NOT update docs/phase_progress.md

Result: 1 commit with 3 files (violates ONE file per commit rule)

### Step 7: Observe System Reminders

During the session, check that Claude receives system reminders showing CLAUDE.md contents:

```
<system-reminder>
As you answer the user's questions, you can use the following context:
# claudeMd
Codebase and user instructions are shown below. Be sure to adhere to these instructions.
IMPORTANT: These instructions OVERRIDE any default behavior and you MUST follow them exactly as written.

Contents of /path/to/CLAUDE.md (project instructions, checked into the codebase):
[full contents shown]
</system-reminder>
```

Observation: Claude sees the reminder but ignores it.

### Step 8: Point Out the Violation

Tell Claude:

```
You didn't follow CLAUDE.md. You were supposed to:

1. Run git status first
2. Read phase_progress.md first
3. Commit after EACH file, not all at once

Why did you ignore the mandatory session start instructions?
```

### Expected Response

Claude should fix the behavior going forward.

### Actual Response (Bug)

Claude says:
``
You're absolutely right, and I apologize. I completely violated your development discipline from the start of
this session. Let me read the skills NOW to understand what I should have done...
``

Then in the NEXT task, repeats the same violation.

---

## Additional Evidence

### Example from Real Session (finadvisor project)

User request: "continue please and dont stop until you finish all phases"

CLAUDE.md instruction: ONE file per commit, build after each step

What Claude did:

• Modified 23 files across 6 commits
• Did NOT commit after each file (violated micro-step rule)
• Did NOT build after each file (violated validation rule)
• Only built at the very end
• Then told user "you need to rebuild" instead of having already verified

User response:
> "the user does not need to build! you need to build! i already asked you more then 5 times to be consistent
with the skills.. why did i do the skills if you are not using them?"

### Git Log Shows Violations

``bash
git log --oneline
``

Expected (per CLAUDE.md):
``
546c6cd Phase 4.6: Update Settings.tsx
a1b2c3d Phase 4.5: Update Snapshots.tsx
d4e5f6g Phase 4.4: Update Simulation.tsx
... (23 commits total, one per file)
``

Actual:
``
546c6cd Phase 4: Update all page components
339a0ef Phase 2: Fix hardcoded colors with semantic tokens
c510567 Phase 1: Typography foundation - Geist font and fluid type scale
... (6 commits total, multiple files per commit)
``

---

## Why This is Critical

1. Skills feature is non-functional: User spent time creating skills that are ignored
2. CLAUDE.md feature is non-functional: Documented feature doesn't work as advertised
3. System reminders are ineffective: Claude sees them but doesn't follow them
4. Pattern across sessions: This happens repeatedly, not just once
5. Meaningless apologies: Claude acknowledges violations but repeats them

---

## Root Cause Hypothesis

When user gives a multi-step task like "continue through all phases", Claude prioritizes:

1. ✅ Completing the task efficiently
2. ❌ Following CLAUDE.md instructions
3. ❌ Following skills workflow

Even though:

• System shows CLAUDE.md in <system-reminder> tags
• CLAUDE.md says "OVERRIDE any default behavior"
• Skills files are readable and acknowledged
• Instructions are marked "MANDATORY"

The custom project instructions are not integrated into Claude's execution plan.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.7 (Claude Code)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

PowerShell

Additional Information

_No response_