CLI Reference¶

PHALUS is CLI-first. Every capability is accessible from the command line; the web UI is a convenience wrapper over the same pipeline.

phalus [COMMAND] [OPTIONS]

Run phalus --help for a summary or phalus [COMMAND] --help for per-command help.

Commands¶

Command	Description
`plan`	Parse a manifest and show what would be processed
`run`	Run the full clean room pipeline from a manifest
`run-one`	Run the pipeline on a single package without a manifest
`inspect`	Inspect a completed job's output directory
`validate`	Re-run validation on an existing output directory
`config`	Print the active configuration (API keys redacted)
`serve`	Start the local web UI

plan¶

Parse a manifest file and display the packages that would be processed. No network calls to registries or LLMs are made. Use this to preview filtering before a long run.

phalus plan <MANIFEST> [OPTIONS]

Arguments¶

Argument	Description
`MANIFEST`	Path to the manifest file (e.g. `package.json`, `requirements.txt`, `Cargo.toml`, `go.mod`)

Options¶

Option	Description
`--only <pkg1,pkg2,...>`	Process only these packages (comma-separated names)
`--exclude <pkg1,pkg2,...>`	Skip these packages (comma-separated names)

Example¶

phalus plan package.json

phalus plan package.json --only lodash,chalk

phalus plan requirements.txt --exclude boto3,botocore

Output:

Manifest: package.json (5 packages, 3 after filtering)

PACKAGE                        VERSION          ECOSYSTEM
-------------------------------------------------------
lodash                         ^4.17.21         npm
express                        ^4.18.2          npm
chalk                          ^5.3.0           npm

run¶

Run the full clean room pipeline for all packages in a manifest. Packages are processed concurrently up to the configured limit.

phalus run <MANIFEST> [OPTIONS]

Arguments¶

Argument	Description
`MANIFEST`	Path to the manifest file

Options¶

Option	Default	Description
`--license <id>`	`mit`	SPDX license identifier for the generated code. Options: `mit`, `apache-2.0`, `bsd-2`, `bsd-3`, `isc`, `unlicense`, `cc0`
`--output <dir>`	`./phalus-output`	Directory to write generated packages
`--only <pkg1,pkg2,...>`	—	Process only these packages
`--exclude <pkg1,pkg2,...>`	—	Skip these packages
`--target-lang <lang>`	Same as source	Reimplement in a different language: `rust`, `go`, `python`, `typescript`
`--isolation <mode>`	`context`	Isolation strategy: `context`, `process`, `container`
`--similarity-threshold <f>`	`0.70`	Similarity score above which a package is flagged as FAIL
`--concurrency <n>`	`3`	Number of packages to process in parallel
`--dry-run`	false	Run Agent A only (produce CSP specs), skip Agent B and validation
`--verbose`	false	Enable verbose logging

Exit codes¶

Code	Meaning
`0`	All packages processed successfully
`1`	One or more packages failed

Examples¶

# Basic run, MIT license
phalus run package.json

# Apache-2.0 output into a specific directory
phalus run package.json --license apache-2.0 --output ./liberated/

# Process only two packages
phalus run package.json --only lodash,express

# Reimplement JavaScript packages in Rust
phalus run package.json --target-lang rust --license apache-2.0

# Dry run: produce specs only, no code generation
phalus run package.json --dry-run

# Stricter similarity threshold
phalus run package.json --similarity-threshold 0.50

# Stronger isolation mode
phalus run package.json --isolation process

run-one¶

Run the clean room pipeline on a single package without needing a manifest file. Useful for quick experiments and testing a specific package.

phalus run-one <PACKAGE> [OPTIONS]

Arguments¶

Argument	Description
`PACKAGE`	Package specification in the format `ecosystem/name@version`. For example: `npm/lodash@4.17.21`, `pypi/requests@2.31.0`, `crates/serde@1.0.193`, `go/github.com/gin-gonic/gin@v1.9.1`

Supported ecosystems: npm, pypi, crates, go.

Options¶

Option	Default	Description
`--license <id>`	`mit`	SPDX license identifier
`--output <dir>`	`./phalus-output`	Output directory
`--target-lang <lang>`	Same as source	Target language: `rust`, `go`, `python`, `typescript`
`--isolation <mode>`	`context`	Isolation mode: `context`, `process`, `container`
`--similarity-threshold <f>`	`0.70`	Similarity threshold
`--verbose`	false	Enable verbose logging

Examples¶

phalus run-one npm/left-pad@1.1.3

phalus run-one npm/lodash@4.17.21 --license apache-2.0

phalus run-one pypi/requests@2.31.0 --output ./py-output/

phalus run-one npm/chalk@5.3.0 --target-lang rust --license mit

phalus run-one crates/serde@1.0.193 --isolation process

inspect¶

Display the contents of a completed job's output directory. With no flags, all sections are shown. Use individual flags to show only what you need.

phalus inspect <OUTPUT_DIR> [OPTIONS]

Arguments¶

Argument	Description
`OUTPUT_DIR`	Path to the output directory written by `run` or `run-one`

Options¶

Option	Description
`--audit`	Show the audit log (timestamp, sequence number, event type per entry)
`--similarity`	Show similarity scores and verdict for each package
`--csp`	Show the CSP document list for each package

If none of --audit, --similarity, or --csp are given, all three sections are shown.

Example¶

# Show everything
phalus inspect ./phalus-output

# Show only similarity scores
phalus inspect ./phalus-output --similarity

# Show only the CSP inventory
phalus inspect ./phalus-output --csp

# Show only the audit log
phalus inspect ./phalus-output --audit

Sample similarity output:

=== Similarity Reports ===
  lodash@4.17.21:
    token_similarity: 0.1200
    name_overlap:     0.8900
    string_overlap:   0.1500
    overall_score:    0.2800
    verdict:          PASS

validate¶

Re-run the validation stage on an existing output directory without regenerating any code. Useful for checking outputs against a different similarity threshold, or after manually reviewing generated files.

phalus validate <OUTPUT_DIR> [OPTIONS]

Arguments¶

Argument	Description
`OUTPUT_DIR`	Path to the output directory to validate

Options¶

Option	Default	Description
`--similarity-threshold <f>`	`0.70`	Similarity threshold for pass/fail

Exit codes¶

Code	Meaning
`0`	All packages passed validation
`1`	One or more packages failed

Example¶

phalus validate ./phalus-output

phalus validate ./phalus-output --similarity-threshold 0.50

Sample output:

PASS lodash (similarity: 0.2800, license: ok)
PASS chalk (similarity: 0.1900, license: ok)
FAIL express (similarity: 0.7200, license: ok)

config¶

Print the active configuration, merging ~/.phalus/config.toml with any PHALUS_* environment variable overrides. API keys are always redacted (shown as ***).

phalus config

No options or arguments.

Example¶

phalus config

Sample output:

[llm]
agent_a_provider = "anthropic"
agent_a_model = "claude-sonnet-4-6"
agent_a_api_key = "***"
agent_a_base_url = ""
agent_b_provider = "anthropic"
agent_b_model = "claude-sonnet-4-6"
agent_b_api_key = "***"
agent_b_base_url = ""

[isolation]
mode = "context"

[limits]
max_packages_per_job = 50
max_package_size_mb = 10
concurrency = 3
...

serve¶

Start the local web UI. The server binds to 127.0.0.1:3000 by default and is accessible only from the local machine.

phalus serve [OPTIONS]

Options¶

Option	Default	Description
`--host <host>`	`127.0.0.1`	Address to bind to
`--port <port>`	`3000`	Port to listen on

Example¶

# Default: localhost only
phalus serve

# Custom port
phalus serve --port 8080

# Bind to all interfaces (use with caution — no authentication)
phalus serve --host 0.0.0.0 --port 3000

After starting, open http://127.0.0.1:3000 in a browser.

See Web UI for a description of the interface and API Reference for the backing REST endpoints.