Package org.egothor.methodatlas.command

package org.egothor.methodatlas.command

CLI command handler implementations for MethodAtlas.

Each class in this package encapsulates one logical CLI mode and implements the Command interface. The thin routing layer in MethodAtlasApp.run(java.lang.String[], java.io.PrintWriter) selects the appropriate command based on the parsed command-line flags and delegates to it via Command.execute(java.io.PrintWriter).

Command handlers

• DiffCommand — -diff
• ScanCommand — CSV / plain-text output (default mode)
• SarifCommand — -sarif
• GitHubAnnotationsCommand — -github-annotations
• ApplyTagsCommand — -apply-tags
• ApplyTagsFromCsvCommand — -apply-tags-from-csv
• ManualPrepareCommand — -manual-prepare

Shared infrastructure

The shared infrastructure that the commands compose is decomposed into a small set of focused collaborators:

• PluginLoader — resolves TestDiscovery and SourcePatcher providers via ServiceLoader and validates plugin-ID uniqueness.
• OverrideLoader — loads classification override YAML files into ClassificationOverride instances.
• ContentHasher — produces SHA-256 class fingerprints and forward-slashed scan-root file prefixes; pure static helpers.
• AiRuntimeBuilder — builds the per-run AI engine, the result cache, and resolves taxonomy metadata.
• ScanOrchestrator — owns the scan-and-emit loop and the apply-tags helpers (collectMethodsByFile, gatherAiSuggestionsForFile, filterSink). Constructed once per CLI run with an injected PluginLoader.

Access conventions

All classes in this package are declared public so that the routing layer in MethodAtlasApp can instantiate them. They are nonetheless considered internal implementation details: callers outside this package should not depend on specific command classes; they should interact only with the Command interface.

Related Packages

Package	Description
org.egothor.methodatlas	Provides the core command-line utility for analyzing Java test sources and producing structured metadata about JUnit test methods.

Class	Description
AiRuntime	Bundle of AI infrastructure that is constant for the duration of a scan run.
AiRuntimeBuilder	Constructs the per-run AI infrastructure: the suggestion engine, the result cache, and the human-readable taxonomy descriptor.
ApplyTagsCommand	CLI command handler for the -apply-tags mode.
ApplyTagsFromCsvCommand	CLI command handler for the -apply-tags-from-csv mode.
CheckPromptsCommand	Utility CLI mode (-check-prompts) that validates prompt templates and prints their SHA-256 checksums without running a scan.
Command	A self-contained CLI command handler.
CommentRedaction	Applies the loaded CommentRedactors to source text on its way to an AI provider, failing closed.
ContentHasher	Pure utility helpers for content fingerprints and scan-root path prefixes.
CredentialScanUnitSource	Selects files to scan for credentials by mask and reads each into a CredentialScanUnit.
DetectCredentialsStage	Runs the deterministic detectors over the scan units, attaches best-effort enclosing-method attribution, and produces CredentialFindings.
DetectCredentialsStage.MethodRange	A method's line span, used for attribution.
DiffCommand	CLI command handler for the -diff mode.
EvalAccuracyCommand	Utility CLI mode (-eval-accuracy) that measures how accurate the AI classification is against a human-reviewed labelled set.
GitHubAnnotationsCommand	CLI command handler for the -github-annotations output mode.
JsonCommand	CLI command handler for the -json output mode.
ManualPrepareCommand	CLI command handler for the -manual-prepare mode.
OverrideLoader	Loads classification override files into ClassificationOverride instances.
PluginLoader	Resolves and configures discovery plugins via ServiceLoader.
RedactionAbortedException	Thrown when -redact-comments is active and comment redaction cannot be guaranteed for a source file, so the run must abort before any source is sent to an AI provider (fail-closed).
SarifCommand	CLI command handler for the -sarif output mode.
ScanCommand	CLI command handler for the default CSV and -plain output modes.
ScanOrchestrator	Orchestrates the scan-and-emit loop that every command mode is built around.