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Allagma

All command flags

Generated from the current CLI parser during the site build. See the CLI overview for behavior and costs.

Allagma

Section titled “Allagma”
usage: allagma [-h] [--version]
               {check,doctor,init,entry,verify,validate-record,verify-evidence,toy,compare,campaign,update,migrate,acceptance,resource,research,reference,paper}
               ...


Portable methods, exact study locks and traceable evidence


positional arguments:
  {check,doctor,init,entry,verify,validate-record,verify-evidence,toy,compare,campaign,update,migrate,acceptance,resource,research,reference,paper}
    check               Check all modules, or only one module's contract
    doctor              Inspect local prerequisites without executing hosts or
                        changing a study
    init                Initialize a study while preserving user-owned files
    entry               Resolve a canonical method from a study or campaign
                        lock
    verify              Verify the study lock, content and intent freshness
    verify-evidence     Read records and their declared references without
                        executing study code
    toy                 Run a complete offline toy study with failure and
                        interruption
    compare             Run the bounded context-method comparison
    acceptance          Generate I1–I5 evidence and a machine-readable report
    resource            Supervise finite study-owned local process budgets
    research            Prepare a reusable brief/material/resource workspace
                        or explicitly run its native workflow
    reference           Maintain an offline critical literature map and frozen
                        reading inputs
    paper               Validate or build an optional evidence-linked arXiv
                        paper; never submit


options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

check

Section titled “check”
usage: allagma check [-h] [--source SOURCE] [--module MODULE]


options:
  -h, --help       show this help message and exit
  --source SOURCE
  --module MODULE

doctor

Section titled “doctor”
usage: allagma doctor [-h] [--source SOURCE] [--study STUDY]
                      [--scope {offline,native}] [--codex CODEX]


options:
  -h, --help            show this help message and exit
  --source SOURCE
  --study STUDY
  --scope {offline,native}
  --codex CODEX         Native executable to inspect, never invoke (with
                        --scope native)

init

Section titled “init”
usage: allagma init [-h] [--source SOURCE] --study STUDY [--id ID]
                    [--intent INTENT]


options:
  -h, --help       show this help message and exit
  --source SOURCE
  --study STUDY
  --id ID
  --intent INTENT

entry

Section titled “entry”
usage: allagma entry [-h] --study STUDY [--campaign CAMPAIGN]
                     [--module MODULE]


options:
  -h, --help           show this help message and exit
  --study STUDY
  --campaign CAMPAIGN
  --module MODULE

verify

Section titled “verify”
usage: allagma verify [-h] --study STUDY


options:
  -h, --help     show this help message and exit
  --study STUDY

validate-record

Section titled “validate-record”
usage: allagma validate-record [-h] path


positional arguments:
  path


options:
  -h, --help  show this help message and exit

verify-evidence

Section titled “verify-evidence”
usage: allagma verify-evidence [-h] --study STUDY --record RECORD
                               [--max-files MAX_FILES] [--max-bytes MAX_BYTES]


options:
  -h, --help            show this help message and exit
  --study STUDY
  --record RECORD       Study-relative JSON record or nonempty record list
  --max-files MAX_FILES
  --max-bytes MAX_BYTES

toy

Section titled “toy”
usage: allagma toy [-h] [--source SOURCE] --destination DESTINATION
                   [--host {generic,codex,claude-code}] [--no-faults]
                   [--context CONTEXT] [--reviewer REVIEWER] [--recipe RECIPE]


options:
  -h, --help            show this help message and exit
  --source SOURCE
  --destination DESTINATION
  --host {generic,codex,claude-code}
  --no-faults
  --context CONTEXT
  --reviewer REVIEWER
  --recipe RECIPE

compare

Section titled “compare”
usage: allagma compare [-h] [--source SOURCE] --output OUTPUT
                       [--baseline BASELINE] [--candidate CANDIDATE]


options:
  -h, --help            show this help message and exit
  --source SOURCE
  --output OUTPUT
  --baseline BASELINE
  --candidate CANDIDATE

campaign

Section titled “campaign”
usage: allagma campaign [-h] --study STUDY --campaign CAMPAIGN
                        [--analysis-id ANALYSIS_ID] [--allow-partial]
                        [--stop-after STOP_AFTER] [--fault-run FAULT_RUN]
                        [--fault-mode {failure,interrupt}]
                        {start,run,analyze,audit,status}


positional arguments:
  {start,run,analyze,audit,status}


options:
  -h, --help            show this help message and exit
  --study STUDY
  --campaign CAMPAIGN
  --analysis-id ANALYSIS_ID
  --allow-partial
  --stop-after STOP_AFTER
  --fault-run FAULT_RUN
  --fault-mode {failure,interrupt}

update

Section titled “update”
usage: allagma update [-h] --study STUDY [--source SOURCE] [--id ID]
                      {check,plan,reconcile,validate,adopt,rollback,recover}


positional arguments:
  {check,plan,reconcile,validate,adopt,rollback,recover}


options:
  -h, --help            show this help message and exit
  --study STUDY
  --source SOURCE
  --id ID

migrate

Section titled “migrate”
usage: allagma migrate [-h] --study STUDY [--spec SPEC] [--id ID]
                       {plan,apply,rollback,recover}


positional arguments:
  {plan,apply,rollback,recover}


options:
  -h, --help            show this help message and exit
  --study STUDY
  --spec SPEC
  --id ID

acceptance

Section titled “acceptance”
usage: allagma acceptance [-h] [--output OUTPUT]


options:
  -h, --help       show this help message and exit
  --output OUTPUT

resource

Section titled “resource”
usage: allagma resource [-h] --ledger LEDGER [--profile PROFILE]
                        [--workdir WORKDIR] [--label LABEL]
                        [--category CATEGORY] [--timeout TIMEOUT] [--attempt]
                        {init,run,status,recover}


positional arguments:
  {init,run,status,recover}


options:
  -h, --help            show this help message and exit
  --ledger LEDGER
  --profile PROFILE
  --workdir WORKDIR
  --label LABEL
  --category CATEGORY
  --timeout TIMEOUT
  --attempt


For run, put the supervised command after --.

research

Section titled “research”
usage: allagma research [-h] [--source SOURCE] --study STUDY --control CONTROL
                        [--brief BRIEF] [--materials MATERIALS]
                        [--profile PROFILE] [--references REFERENCES]
                        [--reference-cache REFERENCE_CACHE]
                        [--paper-config PAPER_CONFIG] [--id ID]
                        [--session SESSION] [--codex CODEX]
                        [--timeout TIMEOUT] [--config CONFIG] [--auth AUTH]
                        [--interrupt-first-attempt] [--baseline]
                        {prepare,run,status}


positional arguments:
  {prepare,run,status}


options:
  -h, --help            show this help message and exit
  --source SOURCE
  --study STUDY
  --control CONTROL
  --brief BRIEF
  --materials MATERIALS
  --profile PROFILE
  --references REFERENCES
                        Critical reference dossier to freeze into preparation
                        inputs
  --reference-cache REFERENCE_CACHE
                        Verified cache for selected execution assets
  --paper-config PAPER_CONFIG
                        Optional paper request with researcher-supplied
                        attribution
  --id ID
  --session SESSION
  --codex CODEX
  --timeout TIMEOUT
  --config CONFIG
  --auth AUTH
  --interrupt-first-attempt
  --baseline            Evaluation control: common infrastructure without
                        Allagma methods

reference

Section titled “reference”
usage: allagma reference [-h] --directory DIRECTORY [--question QUESTION]
                         [--mode {online,offline,provided-only}]
                         [--record RECORD] [--destination DESTINATION]
                         [--require-review] [--cache CACHE] [--online]
                         [--provided PROVIDED] [--policy POLICY]
                         [--approval APPROVAL] [--asset-id ASSET_ID]
                         {init,add,check,index,snapshot,cache-init,acquire,verify-cache,policy,quarantine}


positional arguments:
  {init,add,check,index,snapshot,cache-init,acquire,verify-cache,policy,quarantine}


options:
  -h, --help            show this help message and exit
  --directory DIRECTORY
  --question QUESTION
  --mode {online,offline,provided-only}
  --record RECORD
  --destination DESTINATION
  --require-review
  --cache CACHE
  --online              Explicitly allow acquisition HTTP requests outside
                        scientific workers
  --provided PROVIDED   Local-only JSON mapping of asset IDs to supplied file
                        paths
  --policy POLICY
  --approval APPROVAL
  --asset-id ASSET_ID

paper

Section titled “paper”
usage: allagma paper [-h] --study STUDY [--config CONFIG] [--title TITLE]
                     [--authors AUTHORS] [--destination DESTINATION]
                     [--engine {pdflatex,xelatex}] [--timeout TIMEOUT]
                     {init,check,build}


positional arguments:
  {init,check,build}


options:
  -h, --help            show this help message and exit
  --study STUDY
  --config CONFIG       Defaults to STUDY/paper.json
  --title TITLE
  --authors AUTHORS     Researcher-supplied attribution JSON
  --destination DESTINATION
  --engine {pdflatex,xelatex}
  --timeout TIMEOUT