Index (MethodAtlas)

A B C D E F G H I J K L M N O P R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values

A

Access conventions - Search tag in package org.egothor.methodatlas.command: Section
Activation - Search tag in class org.egothor.methodatlas.JsonLineFormatter: Section
AI-Based Security Tagging - Search tag in package org.egothor.methodatlas: Section
AiCacheEntry - Record Class in org.egothor.methodatlas: One entry of the unified AI result cache: the complete AI answer for a single test class, keyed by the class content hash and tagged with the prompt-catalogue signature that produced it.
AiCacheEntry(String, String, AiClassSuggestion) - Constructor for record class org.egothor.methodatlas.AiCacheEntry: Creates an instance of a AiCacheEntry record class.
aiCacheFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the aiCacheFile record component.
aiCacheOut() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the aiCacheOut record component.
AiCacheStore - Class in org.egothor.methodatlas: Reads and writes the unified AI result cache as a JSON Lines file: one AiCacheEntry per line.
AI-column promotion (risky, opt-in) - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine: Section
AI Enrichment - Search tag in class org.egothor.methodatlas.MethodAtlasApp: Section
aiOptions() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the aiOptions record component.
AiResultCache - Class in org.egothor.methodatlas: In-memory cache of AI results loaded from a previous MethodAtlas run, keyed by the per-class content_hash fingerprint.
AiRuntime - Record Class in org.egothor.methodatlas.command: Bundle of AI infrastructure that is constant for the duration of a scan run.
AiRuntime(AiOptions, AiSuggestionEngine, ClassificationOverride, AiResultCache) - Constructor for record class org.egothor.methodatlas.command.AiRuntime: Creates an instance of a AiRuntime record class.
AiRuntimeBuilder - Class in org.egothor.methodatlas.command: Constructs the per-run AI infrastructure: the suggestion engine, the result cache, and the human-readable taxonomy descriptor.
AiRuntimeBuilder() - Constructor for class org.egothor.methodatlas.command.AiRuntimeBuilder: Creates a new builder.
API shape - Search tag in class org.egothor.methodatlas.command.ScanOrchestrator: Section
apply(Path, List<Path>, int, List<SourcePatcher>, PrintWriter, boolean, boolean) - Static method in class org.egothor.methodatlas.ApplyTagsFromCsvEngine: Applies annotation changes from a reviewed CSV to source files.
applyTags() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the applyTags record component.
ApplyTagsCommand - Class in org.egothor.methodatlas.command: CLI command handler for the -apply-tags mode.
ApplyTagsCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, PluginLoader, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.ApplyTagsCommand: Creates a new apply-tags command.
ApplyTagsFromCsvCommand - Class in org.egothor.methodatlas.command: CLI command handler for the -apply-tags-from-csv mode.
ApplyTagsFromCsvCommand(CliConfig, TestDiscoveryConfig, PluginLoader) - Constructor for class org.egothor.methodatlas.command.ApplyTagsFromCsvCommand: Creates a new apply-tags-from-csv command.
ApplyTagsFromCsvEngine - Class in org.egothor.methodatlas: Engine that applies annotation changes to source files driven by a reviewed MethodAtlas CSV export.
applyTagsFromCsvFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the applyTagsFromCsvFile record component.
asSink() - Method in class org.egothor.methodatlas.coverage.CoverageFacade.Handle: Returns the TestMethodSink that the orchestrator must receive every per-method record on.
ASVS - Enum constant in enum class org.egothor.methodatlas.evidence.EvidenceFramework: OWASP Application Security Verification Standard.

B

beginLine() - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Returns the value of the beginLine record component.
buildCache(Path) - Method in class org.egothor.methodatlas.command.AiRuntimeBuilder: Loads the AI result cache from a previous MethodAtlas CSV output, or returns the empty no-op cache when no cache file was configured.
buildEngine(AiOptions) - Method in class org.egothor.methodatlas.command.AiRuntimeBuilder: Creates the AI suggestion engine for the current run, or returns null when AI support is disabled.

C

cache() - Method in record class org.egothor.methodatlas.command.AiRuntime: Returns the value of the cache record component.
canonicalToken() - Method in enum class org.egothor.methodatlas.evidence.EvidenceFramework: Returns the canonical, case-sensitive token used to identify this framework in pack metadata and on disk.
CheckPromptsCommand - Class in org.egothor.methodatlas.command: Utility CLI mode (-check-prompts) that validates prompt templates and prints their SHA-256 checksums without running a scan.
classification(String, String) - Method in class org.egothor.methodatlas.AiResultCache: Returns the cached classification for a class when the content hash matches and the cached answer is compatible with the current prompt catalogue.
Cleanup - Search tag in class org.egothor.methodatlas.ScanRunContext: Section
clear() - Static method in class org.egothor.methodatlas.ScanRunContext: Removes the current scan run from the calling thread.
CliConfig - Record Class in org.egothor.methodatlas: Parsed command-line configuration used to drive a single application run.
CliConfig(OutputMode, AiOptions, List<Path>, List<String>, Set<String>, Map<String, List<String>>, boolean, ManualMode, boolean, boolean, Path, boolean, Path, boolean, Path, int, boolean, boolean, double, boolean, Path, boolean, Path, Path, String, Path, boolean, Path, String, String, String, boolean, boolean, boolean, String, Path, Path, boolean, boolean, double, double, double, Path) - Constructor for record class org.egothor.methodatlas.CliConfig: Creates an instance of a CliConfig record class.
closeAll(List<TestDiscovery>) - Method in class org.egothor.methodatlas.command.PluginLoader: Closes every provider in the list, logging any IOException at Level.FINE and continuing so that all providers are attempted.
closeAllCredentialDetectors(List<CredentialDetector>) - Method in class org.egothor.methodatlas.command.PluginLoader: Closes every detector in the list, logging any IOException at Level.FINE and continuing so that all detectors are attempted.
collect(List<Path>) - Method in class org.egothor.methodatlas.command.CredentialScanUnitSource: Walks roots and returns one unit per matching, readable file, in deterministic sorted order.
collectMethodsByFile(List<Path>, List<TestDiscovery>) - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Collects all discovered methods from every configured root, keyed by source-file path.
Command - Interface in org.egothor.methodatlas.command: A self-contained CLI command handler.
Command handlers - Search tag in package org.egothor.methodatlas.command: Section
configFingerprint() - Method in record class org.egothor.methodatlas.ScanRun: Returns the value of the configFingerprint record component.
Consume(Path, Path) - Constructor for record class org.egothor.methodatlas.ManualMode.Consume: Creates an instance of a Consume record class.
contentHash() - Method in record class org.egothor.methodatlas.AiCacheEntry: Returns the value of the contentHash record component.
contentHash() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the contentHash record component.
ContentHasher - Class in org.egothor.methodatlas.command: Pure utility helpers for content fingerprints and scan-root path prefixes.
CoverageFacade - Class in org.egothor.methodatlas.coverage: Single public entry point used by MethodAtlasApp to drive -emit-coverage.
CoverageFacade.Handle - Class in org.egothor.methodatlas.coverage: Opaque handle returned by CoverageFacade.prepare(Path, double).
coverageFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the coverageFile record component.
coverageMappingFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the coverageMappingFile record component.
create(String, String) - Static method in record class org.egothor.methodatlas.ScanRun: Creates a new ScanRun with a freshly generated correlation id and the current wall-clock timestamp.
CredentialScanUnitSource - Class in org.egothor.methodatlas.command: Selects files to scan for credentials by mask and reads each into a CredentialScanUnit.
CredentialScanUnitSource(List<String>, String) - Constructor for class org.egothor.methodatlas.command.CredentialScanUnitSource: Creates a source.
current() - Static method in class org.egothor.methodatlas.ScanRunContext: Returns the current scan run for the calling thread, or Optional.empty() when no run is currently set (the standard case before MethodAtlasApp.main(String[]) runs or after ScanRunContext.clear()).

D

DEFAULT_COVERAGE_FILENAME - Static variable in class org.egothor.methodatlas.coverage.CoverageFacade: Default filename used when -coverage-file is not supplied.
DetectCredentialsStage - Class in org.egothor.methodatlas.command: Runs the deterministic detectors over the scan units, attaches best-effort enclosing-method attribution, and produces CredentialFindings.
DetectCredentialsStage(List<CredentialDetector>, Map<Path, List<DetectCredentialsStage.MethodRange>>) - Constructor for class org.egothor.methodatlas.command.DetectCredentialsStage: Creates a stage.
DetectCredentialsStage.MethodRange - Record Class in org.egothor.methodatlas.command: A method's line span, used for attribution.
detectSecrets() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the detectSecrets record component.
DiffCommand - Class in org.egothor.methodatlas.command: CLI command handler for the -diff mode.
DiffCommand(Path, Path) - Constructor for class org.egothor.methodatlas.command.DiffCommand: Creates a new diff command.
driftDetect() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the driftDetect record component.

E

emit(CliConfig, String, String) - Static method in class org.egothor.methodatlas.receipt.ReceiptFacade: Builds and writes a reproducibility receipt for the supplied scan configuration.
emitCoverage() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the emitCoverage record component.
emitMetadata() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the emitMetadata record component.
emitReceipt() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the emitReceipt record component.
emitSourceRoot() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the emitSourceRoot record component.
empty() - Static method in class org.egothor.methodatlas.AiResultCache: Returns an empty cache that always produces misses.
endLine() - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Returns the value of the endLine record component.
engine() - Method in record class org.egothor.methodatlas.command.AiRuntime: Returns the value of the engine record component.
equals(Object) - Method in record class org.egothor.methodatlas.AiCacheEntry: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.CliConfig: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.command.AiRuntime: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.ManualMode.Consume: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.ManualMode.Prepare: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.egothor.methodatlas.ScanRun: Indicates whether some other object is "equal to" this one.
EvidenceFramework - Enum Class in org.egothor.methodatlas.evidence: Compliance frameworks that the -evidence-pack CLI mode can target.
EvidencePackCommand - Class in org.egothor.methodatlas.evidence: Materialises a tamper-evident evidence pack on disk by running one scan and bundling every artefact an auditor needs to verify it later.
EvidencePackCommand(CliConfig, EvidencePackOptions, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.evidence.EvidencePackCommand: Creates a new evidence-pack command.
evidencePackDir() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackDir record component.
evidencePackFramework() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackFramework record component.
evidencePackKeyAlias() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackKeyAlias record component.
evidencePackKeyringEnv() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackKeyringEnv record component.
evidencePackKeyringFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackKeyringFile record component.
EvidencePackOptions - Record Class in org.egothor.methodatlas.evidence: Immutable bag of evidence-pack options collected from the command line.
EvidencePackOptions(EvidenceFramework, Path, boolean, Path, String, String, String) - Constructor for record class org.egothor.methodatlas.evidence.EvidencePackOptions: Creates an instance of a EvidencePackOptions record class.
evidencePackOverwrite() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackOverwrite record component.
evidencePackSignAlgo() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the evidencePackSignAlgo record component.
execute() - Method in class org.egothor.methodatlas.evidence.EvidencePackCommand: Executes the command: runs the scan, writes every pack artefact, and — when a keyring is configured — signs the manifest.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.ApplyTagsCommand: Discovers test methods, gathers AI suggestions, and patches source files.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.ApplyTagsFromCsvCommand: Applies annotation decisions from the reviewed CSV to source files.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.CheckPromptsCommand: Validates each template kind and prints a report.
execute(PrintWriter) - Method in interface org.egothor.methodatlas.command.Command: Executes this command and returns an exit code.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.DiffCommand: Computes and emits the delta between the two scan CSV outputs.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.GitHubAnnotationsCommand: Scans all roots and emits GitHub Actions workflow commands.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.JsonCommand: Scans all roots and emits the buffered result as a JSON array.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.ManualPrepareCommand: Discovers test classes, writes work files, and reports progress.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.SarifCommand: Scans all roots and emits the buffered result as SARIF JSON.
execute(PrintWriter) - Method in class org.egothor.methodatlas.command.ScanCommand: Runs the scan and emits output incrementally.

F

Failure handling - Search tag in class org.egothor.methodatlas.command.AiRuntimeBuilder: Section
Fields - Search tag in record class org.egothor.methodatlas.ScanRun: Section
filePrefix(List<Path>) - Static method in class org.egothor.methodatlas.command.ContentHasher: Derives the forward-slashed path prefix used in GitHub Actions workflow annotations and SARIF location URIs.
fileSuffixes() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the fileSuffixes record component.
filterSink(TestMethodSink, boolean, double, boolean) - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Wraps a TestMethodSink so that only records that pass all active filters are forwarded to delegate.
FLAG_CHECK_PROMPTS - Static variable in class org.egothor.methodatlas.command.CheckPromptsCommand: Flag that selects this utility mode.
FLAG_CLASSIFICATION_PROMPT - Static variable in class org.egothor.methodatlas.command.CheckPromptsCommand: Flag supplying a custom method-classification template file.
FLAG_DEDICATED_TRIAGE_PROMPT - Static variable in class org.egothor.methodatlas.command.CheckPromptsCommand: Flag supplying a custom standalone credential-triage template file.
FLAG_GEN_SIGNING_KEY - Static variable in class org.egothor.methodatlas.evidence.GenSigningKeyCommand: Mode flag that selects this command.
FLAG_TRIAGE_PROMPT - Static variable in class org.egothor.methodatlas.command.CheckPromptsCommand: Flag supplying a custom folded credential-triage appendix template file.
format(LogRecord) - Method in class org.egothor.methodatlas.JsonLineFormatter: Renders record as a single line of JSON terminated by \n.
framework() - Method in class org.egothor.methodatlas.evidence.EvidencePackCommand: Returns the resolved framework name (canonical token).
framework() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the framework record component.
fromArgs(String...) - Static method in class org.egothor.methodatlas.command.CheckPromptsCommand: Builds a command by scanning raw command-line arguments for the three prompt-override flags.

G

gatherAiSuggestionsForFile(Map<String, List<DiscoveredMethod>>, AiRuntime, AiResultCache, Map<String, List<String>>, Map<String, String>) - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Resolves AI security-classification suggestions for every class in byClass and populates tagsToApply and displayNames with the results for methods that are security-relevant.
GenSigningKeyCommand - Class in org.egothor.methodatlas.evidence: CLI command handler for the -gen-signing-key mode, which creates a ZeroEcho keyring containing a fresh signing key pair for evidence-pack signing.
GitHubAnnotationsCommand - Class in org.egothor.methodatlas.command: CLI command handler for the -github-annotations output mode.
GitHubAnnotationsCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.GitHubAnnotationsCommand: Creates a new GitHub Annotations command.

H

hashClass(String) - Static method in class org.egothor.methodatlas.command.ContentHasher: Computes a SHA-256 content fingerprint of a class source string.
hashCode() - Method in record class org.egothor.methodatlas.AiCacheEntry: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.CliConfig: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.command.AiRuntime: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.ManualMode.Consume: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.ManualMode.Prepare: Returns a hash code value for this object.
hashCode() - Method in record class org.egothor.methodatlas.ScanRun: Returns a hash code value for this object.
hashFile(Path) - Static method in class org.egothor.methodatlas.command.ContentHasher: Computes a SHA-256 content fingerprint of the raw bytes of a file.
hits() - Method in class org.egothor.methodatlas.AiResultCache: Returns the number of successful cache lookups so far.

I

Implementation Notes - Search tag in package org.egothor.methodatlas: Section
Invariant - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine: Section
isActive() - Method in class org.egothor.methodatlas.AiResultCache: Returns true when this cache contains at least one entry.
ISO_27001_8_29 - Enum constant in enum class org.egothor.methodatlas.evidence.EvidenceFramework: ISO/IEC 27001:2022 control 8.29 (secure development lifecycle).

J

JsonCommand - Class in org.egothor.methodatlas.command: CLI command handler for the -json output mode.
JsonCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, PluginLoader, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.JsonCommand: Creates a new JSON command.
JsonLineFormatter - Class in org.egothor.methodatlas: Formatter that emits one JSON object per log record, on a single line, suitable for ingestion by log-aggregation pipelines (Elastic, Splunk, Loki) and for reproducible audit-trail archives.
JsonLineFormatter() - Constructor for class org.egothor.methodatlas.JsonLineFormatter: Creates a new formatter.

K

keyAlias() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the keyAlias record component.
Key Capabilities - Search tag in Overview: Section
keyringEnv() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the keyringEnv record component.
keyringFile() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the keyringFile record component.

L

Languages supported for write-back - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine: Section
Languages supported for write-back - Search tag in class org.egothor.methodatlas.command.ApplyTagsCommand: Section
License - Search tag in Overview: Section
Lifecycle - Search tag in class org.egothor.methodatlas.command.PluginLoader: Section
load(Path) - Static method in class org.egothor.methodatlas.AiResultCache: Loads a cache from a unified JSON-Lines cache file or a legacy scan CSV, auto-detected from the file's first non-blank character.
load(Path) - Method in class org.egothor.methodatlas.command.OverrideLoader: Loads the classification override file at the given path, or returns the empty no-op singleton when no override file was configured.
loadCredentialDetectors(CredentialDetectorConfig) - Method in class org.egothor.methodatlas.command.PluginLoader: Loads all CredentialDetector providers registered via ServiceLoader, configures each with config, and returns them in registration order.
loadPatchers(TestDiscoveryConfig) - Method in class org.egothor.methodatlas.command.PluginLoader: Loads all SourcePatcher providers registered via ServiceLoader, configures each one with config, and returns them in registration order.
loadProviders(TestDiscoveryConfig) - Method in class org.egothor.methodatlas.command.PluginLoader: Loads all TestDiscovery providers registered via ServiceLoader, configures each one with config, and returns them in registration order.
looksLikeJsonLines(Path) - Static method in class org.egothor.methodatlas.AiCacheStore: Returns true if file appears to be a unified JSON-Lines cache rather than a legacy scan CSV, by inspecting the first non-whitespace byte.
lookup(String) - Method in class org.egothor.methodatlas.AiResultCache: Returns the cached AI answer for a class by content hash, ignoring the prompt signature.

M

main(String[]) - Static method in class org.egothor.methodatlas.MethodAtlasApp: Program entry point.
Manual AI Workflow - Search tag in class org.egothor.methodatlas.MethodAtlasApp: Section
manualMode() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the manualMode record component.
ManualMode - Interface in org.egothor.methodatlas: Selects between the two phases of the manual AI workflow.
ManualMode.Consume - Record Class in org.egothor.methodatlas: Consume phase: read operator-saved response files and emit enriched CSV.
ManualMode.Prepare - Record Class in org.egothor.methodatlas: Prepare phase: scan source files and write AI prompt work files and empty response stubs.
ManualPrepareCommand - Class in org.egothor.methodatlas.command: CLI command handler for the -manual-prepare mode.
ManualPrepareCommand(ManualMode.Prepare, CliConfig, TestDiscoveryConfig, PluginLoader) - Constructor for class org.egothor.methodatlas.command.ManualPrepareCommand: Creates a new manual-prepare command.
mergeVerdicts(List<CredentialFinding>, Map<Integer, CredentialTriageVerdict>) - Static method in class org.egothor.methodatlas.command.DetectCredentialsStage: Merges LLM triage verdicts into a per-class finding list by candidate index.
method() - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Returns the value of the method record component.
MethodAtlasApp - Class in org.egothor.methodatlas: Command-line entry point that parses the arguments and routes the invocation to the matching Command or utility mode.
MethodRange(String, int, int) - Constructor for record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Creates an instance of a MethodRange record class.
minConfidence() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the minConfidence record component.
Mismatch handling - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine: Section
mismatchLimit() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the mismatchLimit record component.
misses() - Method in class org.egothor.methodatlas.AiResultCache: Returns the number of unsuccessful cache lookups so far.

N

NIST_SSDF_PW8 - Enum constant in enum class org.egothor.methodatlas.evidence.EvidenceFramework: NIST Secure Software Development Framework, practice PW.8.
Null handling - Search tag in class org.egothor.methodatlas.command.OverrideLoader: Section

O

options() - Method in record class org.egothor.methodatlas.command.AiRuntime: Returns the value of the options record component.
org.egothor.methodatlas - package org.egothor.methodatlas: Provides the core command-line utility for analyzing Java test sources and producing structured metadata about JUnit test methods.
org.egothor.methodatlas.command - package org.egothor.methodatlas.command: CLI command handler implementations for MethodAtlas.
org.egothor.methodatlas.coverage - package org.egothor.methodatlas.coverage
org.egothor.methodatlas.evidence - package org.egothor.methodatlas.evidence
org.egothor.methodatlas.receipt - package org.egothor.methodatlas.receipt
outputDir() - Method in class org.egothor.methodatlas.evidence.EvidencePackCommand: Returns the absolute path of the produced pack directory.
outputDir() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the outputDir record component.
Output Formats - Search tag in package org.egothor.methodatlas: Section
outputMode() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the outputMode record component.
Output schema - Search tag in class org.egothor.methodatlas.JsonLineFormatter: Section
override() - Method in record class org.egothor.methodatlas.command.AiRuntime: Returns the value of the override record component.
overrideFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the overrideFile record component.
OverrideLoader - Class in org.egothor.methodatlas.command: Loads classification override files into ClassificationOverride instances.
OverrideLoader() - Constructor for class org.egothor.methodatlas.command.OverrideLoader: Creates a new override loader.
Overview - Search tag in package org.egothor.methodatlas: Section
overwrite() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the overwrite record component.

P

Package Structure - Search tag in Overview: Section
parse(String) - Static method in enum class org.egothor.methodatlas.evidence.EvidenceFramework: Parses a framework token supplied on the command line.
paths() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the paths record component.
PCI_6_4_1 - Enum constant in enum class org.egothor.methodatlas.evidence.EvidenceFramework: PCI DSS requirement 6.4.1 (software security requirements).
PluginLoader - Class in org.egothor.methodatlas.command: Resolves and configures discovery plugins via ServiceLoader.
PluginLoader() - Constructor for class org.egothor.methodatlas.command.PluginLoader: Creates a new plugin loader.
prepare(Path, double) - Static method in class org.egothor.methodatlas.coverage.CoverageFacade: Loads mappingFile and prepares a coverage collector wrapped inside a CoverageFacade.Handle that the CLI can later pass to the scan orchestrator and the writer.
Prepare(Path, Path) - Constructor for record class org.egothor.methodatlas.ManualMode.Prepare: Creates an instance of a Prepare record class.
promoteAi() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the promoteAi record component.
promptSignature() - Method in record class org.egothor.methodatlas.AiCacheEntry: Returns the value of the promptSignature record component.
properties() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the properties record component.

R

read(Path) - Static method in class org.egothor.methodatlas.AiCacheStore: Reads all cache entries from a JSON-Lines file.
ReceiptFacade - Class in org.egothor.methodatlas.receipt: Single public entry point used by MethodAtlasApp to materialise a reproducibility receipt.
receiptFile() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the receiptFile record component.
requireUniqueCredentialDetectorIds(List<CredentialDetector>) - Static method in class org.egothor.methodatlas.command.PluginLoader: Verifies that every CredentialDetector in the list has a unique CredentialDetector.detectorId().
requireUniqueDiscoveryIds(List<TestDiscovery>) - Static method in class org.egothor.methodatlas.command.PluginLoader: Verifies that every TestDiscovery provider in the list has a unique TestDiscovery.pluginId().
requireUniquePatcherIds(List<SourcePatcher>) - Static method in class org.egothor.methodatlas.command.PluginLoader: Verifies that every SourcePatcher in the list has a unique SourcePatcher.pluginId().
resolveTaxonomyInfo(AiOptions, boolean) - Method in class org.egothor.methodatlas.command.AiRuntimeBuilder: Produces a human-readable string identifying which taxonomy configuration is in effect, for inclusion in scan-metadata output.
responseDir() - Method in record class org.egothor.methodatlas.ManualMode.Consume: Returns the value of the responseDir record component.
responseDir() - Method in record class org.egothor.methodatlas.ManualMode.Prepare: Returns the value of the responseDir record component.
run(String[], PrintWriter) - Static method in class org.egothor.methodatlas.evidence.GenSigningKeyCommand: Parses -gen-signing-key arguments and runs the command.
run(List<CredentialScanUnit>) - Method in class org.egothor.methodatlas.command.DetectCredentialsStage: Detects and builds findings for the supplied units, in unit-then-source order.
runDiscovery(Path, List<TestDiscovery>, AiOptions, AiSuggestionEngine, TestMethodSink, boolean, ClassificationOverride, AiResultCache) - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Runs all configured TestDiscovery providers on root, merges their results, orchestrates AI analysis per class, and forwards each method record to sink.
runDiscovery(Path, List<TestDiscovery>, AiOptions, AiSuggestionEngine, TestMethodSink, boolean, ClassificationOverride, AiResultCache, CredentialTriageContext) - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Runs discovery and AI analysis for one root like ScanOrchestrator.runDiscovery(Path, List, AiOptions, AiSuggestionEngine, TestMethodSink, boolean, ClassificationOverride, AiResultCache), additionally folding credential triage into each per-class AI call when secretCtx is supplied.
runId() - Method in record class org.egothor.methodatlas.ScanRun: Returns the value of the runId record component.

S

SarifCommand - Class in org.egothor.methodatlas.command: CLI command handler for the -sarif output mode.
SarifCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.SarifCommand: Creates a new SARIF command.
sarifOmitScores() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the sarifOmitScores record component.
scan(List<Path>, CliConfig, TestDiscoveryConfig, AiSuggestionEngine, TestMethodSink, ClassificationOverride, AiResultCache) - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Scans every configured root, forwarding each discovered test method to sink.
scan(List<Path>, CliConfig, TestDiscoveryConfig, AiSuggestionEngine, TestMethodSink, ClassificationOverride, AiResultCache, CredentialTriageContext) - Method in class org.egothor.methodatlas.command.ScanOrchestrator: Scans every configured root like ScanOrchestrator.scan(List, CliConfig, TestDiscoveryConfig, AiSuggestionEngine, TestMethodSink, ClassificationOverride, AiResultCache), additionally folding credential triage into each per-class AI call when secretCtx is supplied, so the class source is sent to the provider once for both classification and triage.
ScanCommand - Class in org.egothor.methodatlas.command: CLI command handler for the default CSV and -plain output modes.
ScanCommand(CliConfig, TestDiscoveryConfig, AiSuggestionEngine, ClassificationOverride, AiResultCache, PluginLoader, ScanOrchestrator) - Constructor for class org.egothor.methodatlas.command.ScanCommand: Creates a new scan command.
ScanOrchestrator - Class in org.egothor.methodatlas.command: Orchestrates the scan-and-emit loop that every command mode is built around.
ScanOrchestrator(PluginLoader) - Constructor for class org.egothor.methodatlas.command.ScanOrchestrator: Creates a new orchestrator with no extra sink.
ScanOrchestrator(PluginLoader, Optional<TestMethodSink>) - Constructor for class org.egothor.methodatlas.command.ScanOrchestrator: Creates a new orchestrator that fans out every record to extraSink in addition to the command's primary sink.
ScanRun - Record Class in org.egothor.methodatlas: Immutable record identifying one CLI invocation of MethodAtlas.
ScanRun(String, Instant, String, String) - Constructor for record class org.egothor.methodatlas.ScanRun: Compact constructor enforcing the documented invariants on the component values.
ScanRunContext - Class in org.egothor.methodatlas: Thread-local holder for the current ScanRun, the JUL-friendly equivalent of SLF4J's MDC.
secretsErrorThreshold() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsErrorThreshold record component.
secretsInclude() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsInclude record component.
secretsMinScore() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsMinScore record component.
secretsOut() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsOut record component.
secretsRules() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsRules record component.
secretsSeparateLlm() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsSeparateLlm record component.
secretsShowValues() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsShowValues record component.
secretsWarningThreshold() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the secretsWarningThreshold record component.
securityOnly() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the securityOnly record component.
set(ScanRun) - Static method in class org.egothor.methodatlas.ScanRunContext: Sets the current scan run for the calling thread.
Shared infrastructure - Search tag in package org.egothor.methodatlas.command: Section
signatureAlgorithm() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns the value of the signatureAlgorithm record component.
Source-Derived Metadata - Search tag in class org.egothor.methodatlas.MethodAtlasApp: Section
startedAt() - Method in record class org.egothor.methodatlas.ScanRun: Returns the value of the startedAt record component.
Sub-packages - Search tag in package org.egothor.methodatlas: Section
suggestion() - Method in record class org.egothor.methodatlas.AiCacheEntry: Returns the value of the suggestion record component.
Supported Command-Line Options - Search tag in class org.egothor.methodatlas.MethodAtlasApp: Section

T

testMarkers() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the testMarkers record component.
Thread safety - Search tag in class org.egothor.methodatlas.JsonLineFormatter: Section
Thread safety - Search tag in class org.egothor.methodatlas.ScanRunContext: Section
Thread safety - Search tag in class org.egothor.methodatlas.command.OverrideLoader: Section
Thread safety - Search tag in class org.egothor.methodatlas.command.PluginLoader: Section
Thread safety - Search tag in class org.egothor.methodatlas.command.ScanOrchestrator: Section
toolVersion() - Method in record class org.egothor.methodatlas.ScanRun: Returns the value of the toolVersion record component.
toString() - Method in record class org.egothor.methodatlas.AiCacheEntry: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.CliConfig: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.command.AiRuntime: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.command.DetectCredentialsStage.MethodRange: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.evidence.EvidencePackOptions: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.ManualMode.Consume: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.ManualMode.Prepare: Returns a string representation of this record class.
toString() - Method in record class org.egothor.methodatlas.ScanRun: Returns a string representation of this record class.
toTargetMethod(DiscoveredMethod) - Static method in class org.egothor.methodatlas.command.ScanOrchestrator: Converts a single discovered test method into a prompt target descriptor.
Typical Usage - Search tag in package org.egothor.methodatlas: Section

U

Usage - Search tag in class org.egothor.methodatlas.evidence.GenSigningKeyCommand: Section

V

valueOf(String) - Static method in enum class org.egothor.methodatlas.evidence.EvidenceFramework: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.egothor.methodatlas.evidence.EvidenceFramework: Returns an array containing the constants of this enum class, in the order they are declared.
verbose() - Method in record class org.egothor.methodatlas.CliConfig: Returns the value of the verbose record component.
verdicts(String, String) - Method in class org.egothor.methodatlas.AiResultCache: Returns cached credential-triage verdicts for a class when the content hash and the prompt signature both match and verdicts were actually recorded.

W

What is applied - Search tag in class org.egothor.methodatlas.ApplyTagsFromCsvEngine: Section
workDir() - Method in record class org.egothor.methodatlas.ManualMode.Consume: Returns the value of the workDir record component.
workDir() - Method in record class org.egothor.methodatlas.ManualMode.Prepare: Returns the value of the workDir record component.
write(String, Path) - Method in class org.egothor.methodatlas.coverage.CoverageFacade.Handle: Builds the report and writes it to outputFile.
write(Path, Collection<AiCacheEntry>) - Static method in class org.egothor.methodatlas.AiCacheStore: Writes cache entries to a JSON-Lines file, one entry per line, overwriting any existing file.

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