doctor enhancements, setup, enhancements, ui functionality and design consolidation and , test projects fixes , product advisory attestation/rekor and delta verfications enhancements

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# CLI Migration Guide: v2.x to v3.0
This guide documents the CLI command consolidation that begins in v2.x (with deprecation warnings) and completes in v3.0 (old commands removed).
---
## Overview
The Stella CLI has been reorganized for better discoverability and consistency:
| Change | Reason |
|--------|--------|
| 81+ top-level commands → 18 | Easier to discover and remember |
| Scattered settings → `stella config` | Unified configuration management |
| Multiple verify commands → `stella verify` | Consistent verification interface |
| Compound names → proper hierarchy | `scangraph``scan graph` |
## Deprecation Timeline
- **v2.x**: Old commands work but show deprecation warnings
- **v3.0**: Old commands removed
To suppress deprecation warnings during transition:
```bash
export STELLA_SUPPRESS_DEPRECATION_WARNINGS=1
```
---
## Quick Migration Reference
### Settings & Configuration
```bash
# Before (deprecated)
stella notify channels list
stella admin feeds status
stella registry list
# After
stella config notify channels list
stella config feeds status
stella config registry list
```
### Verification
```bash
# Before (deprecated)
stella attest verify <artifact>
stella vex verify <artifact>
stella patchverify <artifact>
# After
stella verify attestation <artifact>
stella verify vex <artifact>
stella verify patch <artifact>
```
### Scanning
```bash
# Before (deprecated)
stella scangraph list
stella secrets bundle create <dir>
stella image inspect <ref>
# After
stella scan graph list
stella scan secrets bundle create <dir>
stella scan image inspect <ref>
```
### Evidence & Audit
```bash
# Before (deprecated)
stella evidenceholds list
stella audit export
stella prove --artifact <ref>
stella replay run
# After
stella evidence holds list
stella evidence audit export
stella evidence proof generate --artifact <ref>
stella evidence replay run
```
### Reachability
```bash
# Before (deprecated)
stella reachgraph list
stella slice create
stella witness show <path>
# After
stella reachability graph list
stella reachability slice create
stella reachability witness show <path>
```
### SBOM
```bash
# Before (deprecated)
stella sbomer compose
stella layersbom show <digest>
# After
stella sbom compose
stella sbom layer show <digest>
```
### Cryptography
```bash
# Before (deprecated)
stella keys list
stella issuerkeys list
stella sign image <ref>
# After
stella crypto keys list
stella crypto keys issuer list
stella crypto sign image <ref>
```
### Administration
```bash
# Before (deprecated)
stella doctor run
stella db migrate
stella admin users list
# After
stella admin doctor run
stella admin db migrate
stella auth users list
```
### CI/CD
```bash
# Before (deprecated)
stella gate evaluate
stella github upload
# After (either works)
stella release gate evaluate
stella ci gate evaluate # shortcut for CI pipelines
stella ci github upload
```
### Utilities
```bash
# Before (deprecated)
stella binary diff
stella hlc show
stella timeline query
# After
stella tools binary diff
stella tools hlc show
stella tools timeline query
```
---
## New Command Structure
### Primary Commands
```
stella scan # Scanning operations
stella release # Release management
stella verify # All verification
stella attest # Create attestations
stella evidence # Evidence management
stella policy # Policy management
stella vex # VEX operations
stella reachability # Reachability analysis
stella sbom # SBOM operations
stella crypto # Cryptography
stella config # Settings & configuration
stella auth # Authentication
stella admin # Administration
stella ci # CI/CD integration
stella setup # Initial setup
stella explain # Explain decisions
stella tools # Utility commands
```
### `stella config` - Unified Settings
All configuration is now under `stella config`:
```
stella config
├── list [--category <cat>] # List config paths
├── show <path> # Show config value
├── set <path> <value> # Set config value
├── export # Export all config
├── import <file> # Import config
├── notify/ # Notification settings
│ ├── channels list/test
│ ├── templates list/render
│ └── preferences export/import
├── feeds/ # Feed configuration
│ ├── list
│ ├── status
│ └── refresh
├── integrations/ # Integration settings
│ ├── list
│ └── test
├── registry/ # Registry settings
└── sources/ # Data sources
```
### `stella verify` - Unified Verification
All verification under one command:
```
stella verify
├── image <ref> # Image attestation
├── bundle <path> # Evidence bundle
├── offline <artifact> # Offline verification
├── attestation <artifact> # Attestation verification
├── vex <artifact> # VEX verification
├── patch <artifact> # Patch verification
└── sbom <file> # SBOM verification
```
### `stella scan` - Unified Scanning
All scanning under one command:
```
stella scan
├── run <ref> # Run a scan
├── status <id> # Check status
├── results <id> # View results
├── download # Download scanner bundle
├── workers # Configure workers
├── graph/ # Scan graph operations
├── secrets/ # Secret detection
│ └── bundle create/verify/info
└── image/ # Image analysis
├── inspect
└── layers
```
---
## CI/CD Script Updates
### GitHub Actions
```yaml
# Before
- run: stella gate evaluate --artifact ${{ env.IMAGE_SHA }}
# After (either works)
- run: stella ci gate evaluate --artifact ${{ env.IMAGE_SHA }}
# or
- run: stella release gate evaluate --artifact ${{ env.IMAGE_SHA }}
```
### GitLab CI
```yaml
# Before
script:
- stella notify channels test --channel slack-alerts
# After
script:
- stella config notify channels test --channel slack-alerts
```
### Jenkins
```groovy
// Before
sh 'stella scangraph list --format json'
// After
sh 'stella scan graph list --format json'
```
---
## Common Errors and Solutions
### "Command not found" in v3.0
If upgrading to v3.0 and a command fails:
```bash
$ stella scangraph list
Error: Unknown command 'scangraph'. Did you mean 'scan graph'?
```
Update your script to use the new path.
### "Deprecated command" warnings
```
WARNING: 'stella notify' is deprecated and will be removed in v3.0.
Use 'stella config notify' instead.
```
This is informational. The command still works but should be updated.
### Suppressing warnings in CI
```bash
export STELLA_SUPPRESS_DEPRECATION_WARNINGS=1
stella notify channels list # No warning
```
---
## Getting Help
```bash
# See all commands
stella --help
# See subcommands
stella config --help
stella verify --help
# See command details
stella config notify channels list --help
```
---
## Migration Checklist
- [ ] Update CI/CD pipelines to use new command paths
- [ ] Update documentation referencing CLI commands
- [ ] Update automation scripts
- [ ] Test with `STELLA_SUPPRESS_DEPRECATION_WARNINGS=0` to find deprecated usage
- [ ] Plan upgrade to v3.0 before end-of-support for v2.x