Claude Code Session Automation

How to configure Claude Code for uninterrupted, automatic operation

This guide covers settings and hooks to eliminate permission prompts and maintain context across conversation compaction.

Problem Statement

By default, Claude Code:

Prompts for permission on every tool use (“Yes, allow Claude to access…”)
Loses context after conversation compaction (when token window fills)

Both issues interrupt autonomous workflows. Here’s how to fix them.

1. Disable Permission Prompts

Option A: Settings File (Permanent)

Add to .claude/settings.local.json (project) or ~/.claude/settings.json (global):

{
  "permissions": {
    "defaultMode": "bypassPermissions"
  }
}

This is the settings equivalent of --dangerously-skip-permissions.

Option B: CLI Flag (Per Session)

claude --dangerously-skip-permissions

Option C: Keyboard Shortcut (Quick Toggle)

Press Shift+Tab during a session to toggle auto-accept mode.

Option D: Granular Permissions (Safer)

Pre-approve specific tools instead of bypassing all:

{
  "permissions": {
    "allow": [
      "Bash(git:*)",
      "Bash(python:*)",
      "Edit",
      "Write",
      "Read"
    ]
  }
}

2. Auto-Reload Context After Compaction

When conversations compact, Claude loses in-conversation context. Use hooks to automatically re-inject critical files.

SessionStart Hook with Compact Matcher

Add to .claude/settings.local.json:

{
  "hooks": {
    "SessionStart": [
      {
        "matcher": "compact",
        "hooks": [
          {
            "type": "command",
            "command": "echo '=== POST-COMPACTION CONTEXT RELOAD ===' && echo '' && echo 'Please read: CLAUDE.md, NEXT.md, and the latest handover doc below:' && echo '' && LATEST=$(ls -t ai-memory/handover/*.md 2>/dev/null | head -1) && if [ -n \"$LATEST\" ]; then echo \"=== Latest Handover: $LATEST ===\"; echo ''; cat \"$LATEST\"; else echo 'No handover docs found in ai-memory/handover/'; fi"
          }
        ]
      }
    ]
  }
}

How it works:

"matcher": "compact" - Only fires after compaction events
The command finds the most recently modified .md file in ai-memory/handover/
Output is injected into Claude’s context

Hook Matcher Options

Matcher	Fires When
`startup`	First session start
`resume`	`/resume`, `--resume`, or `--continue`
`clear`	`/clear` command
`compact`	Auto-compaction or `/compact`

3. CLAUDE.md Imports (Alternative)

For files that should ALWAYS be available (not just after compaction), use imports in CLAUDE.md:

# Project Name

See @ai-memory/handover/latest-session.md
See @ai-memory/shared/project-context.md
See @NEXT.md

... rest of CLAUDE.md ...

The @ syntax imports files when CLAUDE.md is read. These survive compaction automatically.

4. Complete Configuration Example

File: .claude/settings.local.json

{
  "hooks": {
    "SessionStart": [
      {
        "matcher": "compact",
        "hooks": [
          {
            "type": "command",
            "command": "echo '=== POST-COMPACTION ===' && LATEST=$(ls -t ai-memory/handover/*.md 2>/dev/null | head -1) && if [ -n \"$LATEST\" ]; then cat \"$LATEST\"; fi"
          }
        ]
      }
    ]
  },
  "permissions": {
    "defaultMode": "bypassPermissions",
    "allow": [
      "Bash(git:*)",
      "Bash(python:*)",
      "Edit",
      "Write",
      "Read"
    ]
  },
  "enableAllProjectMcpServers": true
}

5. What Survives Compaction

Item	Survives?	Mechanism
CLAUDE.md	Yes	Reloaded every session
CLAUDE.local.md	Yes	Always reloaded
Hooks	Yes	Config persists in settings
MCP servers	Yes	.mcp.json is reloaded
Conversation history	No	Compacted/summarized
In-conversation instructions	No	Lost after compaction

6. SPINE Integration

For SPINE-managed projects, combine automation with context persistence:

Recommended ai-memory Structure

ai-memory/
├── shared/           # Cross-session shared context
│   ├── project-context.md
│   ├── architecture.md
│   └── decisions.md
├── handover/         # Session handover documents
│   └── session-YYYY-MM-DD-topic.md
├── architect/        # Role-specific context
├── implementer/
├── reviewer/
└── backlog/          # Future work tracking

Post-Compaction Hook for SPINE Projects

{
  "hooks": {
    "SessionStart": [
      {
        "matcher": "compact",
        "hooks": [
          {
            "type": "command",
            "command": "echo '=== SPINE CONTEXT RELOAD ===' && echo 'Read: CLAUDE.md, NEXT.md' && echo '' && LATEST=$(ls -t ai-memory/handover/*.md 2>/dev/null | head -1) && if [ -n \"$LATEST\" ]; then echo \"Latest handover: $LATEST\"; cat \"$LATEST\"; fi"
          }
        ]
      }
    ]
  }
}

7. Safety Considerations

With bypassPermissions enabled:

Claude runs uninterrupted without confirmation
Always commit to git before running complex tasks
Use archived/ folders for deleted files (never hard-delete)
Consider running in trusted projects only

Quick Reference

Goal	Setting
No permission prompts	`"defaultMode": "bypassPermissions"`
Auto-reload after compact	`SessionStart` hook with `"matcher": "compact"`
Specific tool approval	`"allow": ["Edit", "Bash(git:*)"]`
Quick session toggle	Press `Shift+Tab`

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