Update usability and repo clarity

.gitignore

@@ -1,4 +1,5 @@
 /!!!temp/
+/heap/
 /AlgTest_JavaCard/nbproject/private/*
 /AlgTest_JavaCard/!uploader/*
 /AlgTest_JavaCard/build/*
@@ -12,7 +13,8 @@
 /AlgTest_JClient/test/*.jar
 /AlgTest_JClient/dist/*
 /AlgTest_JClient/nbproject/*
-
+/AlgTest_JClient/*.log
+/AlgTest_JClient/store/*
 
 /AlgTest_Process/dist/*
 /AlgTest_Process/test-output/*

AlgTest_JClient/nbproject/build-impl.xml

@@ -20,6 +20,7 @@ is divided into following sections:
 
         -->
 <project xmlns:if="ant:if" xmlns:j2seproject1="http://www.netbeans.org/ns/j2se-project/1" xmlns:j2seproject3="http://www.netbeans.org/ns/j2se-project/3" xmlns:jaxrpc="http://www.netbeans.org/ns/j2se-project/jax-rpc" xmlns:unless="ant:unless" basedir=".." default="default" name="AlgTestJClient-impl">
+    <import file="build-native.xml"/>
     <fail message="Please build using Ant 1.8.0 or higher.">
         <condition>
             <not>

AlgTest_JClient/nbproject/genfiles.properties

@@ -3,6 +3,6 @@ build.xml.script.CRC32=04cacdaf
 build.xml.stylesheet.CRC32=8064a381@1.68.1.46
 # This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
 # Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
-nbproject/build-impl.xml.data.CRC32=168c3420
-nbproject/build-impl.xml.script.CRC32=eefd4347
-nbproject/build-impl.xml.stylesheet.CRC32=12e0a6c2@1.100.0.48
+nbproject/build-impl.xml.data.CRC32=62d418e4
+nbproject/build-impl.xml.script.CRC32=098dc93d
+nbproject/build-impl.xml.stylesheet.CRC32=12e0a6c2@1.101.0.48

AlgTest_JClient/nbproject/project.properties

@@ -38,7 +38,7 @@ file.reference.is-native-c.jar=libs\\JNA\\is-native-c.jar
 file.reference.is-runtime.jar=libs\\JNA\\is-runtime.jar
 file.reference.jcardsim-2.2.2-all.jar=test\\jcardsim-2.2.2-all.jar
 file.reference.jcardsim-3.0.4.jar=jcardsim-3.0.4.jar
-file.reference.jcardsim-3.0.5-SNAPSHOT.jar=..\\libs\\jcardsim-3.0.5-SNAPSHOT.jar
+file.reference.jcardsim-3.0.6.0.jar=libs/jcardsim-3.0.6.0.jar
 file.reference.jcommander-1.81.jar=../libs/jcommander-1.81.jar
 file.reference.jctasks.jar=libs\\JNA\\jctasks.jar
 file.reference.jna-4.1.0.jar=libs\\JNA\\jna-4.1.0.jar
@@ -55,9 +55,9 @@ javac.classpath=\
     ${file.reference.jna-4.1.0.jar}:\
     ${file.reference.jna-platform-4.1.0.jar}:\
     ${file.reference.jna.jar}:\
-    ${file.reference.jcardsim-3.0.5-SNAPSHOT.jar}:\
     ${file.reference.jcommander-1.81.jar}:\
-    ${file.reference.jcommander-1.81.jar}
+    ${file.reference.jcommander-1.81.jar}:\
+    ${file.reference.jcardsim-3.0.6.0.jar}
 # Space-separated list of extra javac options
 javac.compilerargs=
 javac.deprecation=false
@@ -114,6 +114,7 @@ manifest.custom.permissions=
 manifest.file=manifest.mf
 meta.inf.dir=${src.dir}/META-INF
 mkdist.disabled=false
+native.bundling.enabled=true
 platform.active=default_platform
 run.classpath=\
     ${javac.classpath}:\

AlgTest_JClient/nbproject/project.xml

@@ -2,6 +2,9 @@
 <project xmlns="http://www.netbeans.org/ns/project/1">
     <type>org.netbeans.modules.java.j2seproject</type>
     <configuration>
+        <buildExtensions xmlns="http://www.netbeans.org/ns/ant-build-extender/1">
+            <extension file="build-native.xml" id="j2sedeploy"/>
+        </buildExtensions>
         <data xmlns="http://www.netbeans.org/ns/j2se-project/3">
             <name>AlgTestJClient</name>
             <source-roots>

AlgTest_JClient/src/algtestjclient/AlgTestJClient.java

@@ -57,6 +57,7 @@ public class AlgTestJClient {
      * Version 1.8.3 (10.02.2026)
      * - Fix incorrect testing of OneShot engines
      * - print used command line arguments into log
+     * - More detailed help
      */
     public final static String ALGTEST_JCLIENT_VERSION = "1.8.3";
     /**
@@ -200,6 +201,20 @@ public class AlgTestJClient {
 
     static DirtyLogger m_SystemOutLogger = null;
     public static void main(String[] args) throws IOException, Exception {
+        try {
+            runMain(args);
+        } catch (Exception ex) {
+            System.err.println("\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!");
+            System.err.println("Unexpected error: " + ex.getMessage());
+            System.err.println("\nIf this error is unexpected, please report it at:");
+            System.err.println("  https://github.com/crocs-muni/JCAlgTest/issues");
+            System.err.println("Include: your OS, Java version, card ATR, and the .log file from this directory.");
+            System.err.println("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
+            throw ex;
+        }
+    }
+
+    static void runMain(String[] args) throws IOException, Exception {
         Map<String, String> tempInfo = new HashMap<>();
 
         Args cmdArgs = new Args();
@@ -221,7 +236,7 @@ public static void main(String[] args) throws IOException, Exception {
         FileOutputStream    systemOutLogger = new FileOutputStream(logFileName);
         tempInfo.put("out_file_name", logFileName);
         allResultsMap.put("main", tempInfo);
-        m_SystemOutLogger = new DirtyLogger(systemOutLogger, true);
+        m_SystemOutLogger = new DirtyLogger(systemOutLogger, true, cmdArgs.verbose);
 
         m_SystemOutLogger.print("Command line arguments: ");
         for (int i = 0; i < args.length; i++) {
@@ -245,7 +260,8 @@ public static void main(String[] args) throws IOException, Exception {
         m_SystemOutLogger.println();
 
         if (cmdArgs.help) {
-            JCommander.newBuilder().addObject(cmdArgs).build().usage();     
+            JCommander.newBuilder().addObject(cmdArgs).build().usage();
+            printHelpExtras();
             return;
         }
 
@@ -364,9 +380,37 @@ else if (operation.compareTo(Args.OP_ALG_FINGERPRINT) == 0) {
 
         if (cmdArgs.selftest) {
             checkSelfTestResults(allResultsMap);
-        }   
+        }
     }
-
+
+    static void printHelpExtras() {
+        System.out.println("\nExamples:");
+        System.out.println("  # Interactive mode — prompts for reader and test selection:");
+        System.out.println("  java -jar AlgTestJClient.jar\n");
+        System.out.println("  # Interactive mode with simulator — prompts for test selection with simulated card as target:");
+        System.out.println("  java -jar AlgTestJClient.jar -simulator\n");
+        System.out.println("  # Test which algorithms the card supports (non-interactive):");
+        System.out.println("  java -jar AlgTestJClient.jar -op ALG_SUPPORT_EXTENDED -cardname MyCard -fresh\n");
+        System.out.println("  # Fixed-length performance benchmark:");
+        System.out.println("  java -jar AlgTestJClient.jar -op ALG_PERFORMANCE_STATIC -cardname MyCard -fresh\n");
+        System.out.println("  # Variable-length performance benchmark, save results to /tmp/:");
+        System.out.println("  java -jar AlgTestJClient.jar -op ALG_PERFORMANCE_VARIABLE -cardname MyCard -fresh -outpath /tmp/\n");
+        System.out.println("  # Show full per-algorithm detail on console:");
+        System.out.println("  java -jar AlgTestJClient.jar -op ALG_SUPPORT_EXTENDED -cardname MyCard -fresh -verbose\n");
+        System.out.println("Common problems:");
+        System.out.println("  Card not found     -- Is the PC/SC daemon running? On Linux: sudo pcscd");
+        System.out.println("                        On Linux you may also need:");
+        System.out.println("                        -Dsun.security.smartcardio.library=/usr/lib64/libpcsclite.so.1");
+        System.out.println("  Testing hangs      -- The card may not support this algorithm; see KNOWN_ISSUES.md.");
+        System.out.println("                        Re-insert the card and re-run with -fresh to skip ahead.");
+        System.out.println("  Results incomplete -- Re-run with -fresh to discard partial results and start over.");
+        System.out.println("  Console too noisy  -- Run with -verbose only when debugging; default shows high-level");
+        System.out.println("                        progress only; full detail is always saved to the .log file.\n");
+        System.out.println("Reporting bugs:");
+        System.out.println("  https://github.com/crocs-muni/JCAlgTest/issues");
+        System.out.println("  Include: OS, Java version, card ATR, and the .log file from this directory.\n");
+    }
+
     static long getStartTime() {
         if (m_appStartTime == 0) {
             m_appStartTime = System.currentTimeMillis();
@@ -375,6 +419,10 @@ static long getStartTime() {
     }
 
     static void printSendRequest() {
+        System.out.println("\n=========================================");
+        System.out.println("Testing complete.");
+        System.out.println("Results written to the current directory (*.csv and *.log).");
+        System.out.println("=========================================");
         System.out.println("\n-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*");
         System.out.println("KIND REQUEST: Please consider sending us your results to extend info openly");
         System.out.println("available to all JavaCard enthusiasts at http://jcalgtest.org.");

AlgTest_JClient/src/algtestjclient/Args.java

@@ -42,5 +42,8 @@ public class Args {
 
     @Parameter(names = "-selftest", description = "Executes selftesting using simulator as target.")
     public boolean selftest = false;
-
+
+    @Parameter(names = "-verbose", description = "Show detailed per-algorithm output on console (default: detail is written to log file only)")
+    public boolean verbose = false;
+
 }

AlgTest_JClient/src/algtestjclient/DirtyLogger.java

@@ -40,10 +40,19 @@ may be distributed under the terms of the GNU General Public License (GPL),
 public class DirtyLogger {
     FileOutputStream    m_logFile;
     boolean             m_bOutputSystemOut = true;
+    boolean             m_verbose = false;
+
     public DirtyLogger(FileOutputStream logFile, boolean bOutputSystemOut) {
         m_logFile = logFile;
         m_bOutputSystemOut = bOutputSystemOut;
     }
+
+    public DirtyLogger(FileOutputStream logFile, boolean bOutputSystemOut, boolean verbose) {
+        m_logFile = logFile;
+        m_bOutputSystemOut = bOutputSystemOut;
+        m_verbose = verbose;
+    }
+
     public void println() {
         String logLine = "\n";
         print(logLine);
@@ -62,5 +71,27 @@ public void print(String logLine) {
             } catch (IOException ex) {
             }
         }
-    }    
+    }
+
+    /**
+     * Detail-level output: always written to the log file, but printed to
+     * the console only when the -verbose flag is active.  Use this for
+     * per-algorithm APDU traces and low-level status lines that would
+     * otherwise flood the console during a long test run.
+     */
+    public void printlnDetail(String logLine) {
+        printDetail(logLine + "\n");
+    }
+
+    public void printDetail(String logLine) {
+        if (m_bOutputSystemOut && m_verbose) {
+            System.out.print(logLine);
+        }
+        if (m_logFile != null) {
+            try {
+                m_logFile.write(logLine.getBytes());
+            } catch (IOException ex) {
+            }
+        }
+    }
 }

AlgTest_JClient/src/algtestjclient/PerformanceTesting.java

@@ -518,10 +518,11 @@ void finalizeMeasurement(Map<String, String> results) throws IOException {
         }
         if (results != null) { results.put("errors_observed", String.format("%d", totalErrors)); } 
 
-        message = "\n\nCard used: " + m_cardName; 
+        message = "\n\nCard used: " + m_cardName;
         m_SystemOutLogger.println(message);
+
     }
-    
+
     void LoadAlreadyMeasuredAlgs(String cardName, String testType, boolean bForceFreshmeasurement) {
         String filePath = testType + "_already_measured.list";
         String filePathOld = filePath + ".old";
@@ -965,28 +966,38 @@ public double perftest_measure(byte appletCLA, byte appletPrepareINS, byte apple
                     return -1;
                 }
                 catch (Exception ex) {
-                    // Unexpected exception
-                    m_SystemOutLogger.println(ex.toString() + "\n"); 
-                    numFailedRepeats++; 
-
+                    // Unexpected exception — likely card removed or communication failure
+                    String exClass = ex.getClass().getSimpleName();
+                    boolean isCardRemoved = (ex instanceof javax.smartcardio.CardNotPresentException)
+                            || exClass.contains("CardNotPresent")
+                            || (ex.getMessage() != null && (ex.getMessage().contains("SCARD_E_NO_SMARTCARD")
+                                || ex.getMessage().contains("no card")));
+                    if (isCardRemoved) {
+                        m_SystemOutLogger.println("ERROR: Card removed or communication lost during '" + info + "'. Attempting to reconnect...");
+                    } else {
+                        m_SystemOutLogger.println("ERROR: Unexpected exception (" + exClass + ") during '" + info + "': " + ex.getMessage());
+                    }
+                    numFailedRepeats++;
+
                     if (numFailedRepeats == 1) {
                         // For first fail, try to reconnect to card automatically
                         try {
                             m_numReconnects++;
                             m_cardManager.ConnectToCard();
                         }
                         catch (Exception ex2) {
-                            m_SystemOutLogger.println(ex2.toString()); 
+                            m_SystemOutLogger.println(ex2.toString());
                             numFailedRepeats++;
                         }
                     }
-                    
+
                     if (numFailedRepeats > 1) {
-                        // For second fail, ask user 
-                        m_SystemOutLogger.println("ERROR: unable to measure operation '" + info + "' properly because of exception (" + ex.toString() + ")");
-                        m_SystemOutLogger.println("Current reader is: " + m_cardManager.getTerminalName());
-                        m_SystemOutLogger.println("Current card is: " + m_cardName + " - " + m_cardManager.getATR());
-                        m_SystemOutLogger.println("Try to physically remove card and/or upload applet manually and insert it again. Press 'r' to retry or 's' to skip this algorithm (if retry fails)\n");
+                        // For second fail, ask user
+                        m_SystemOutLogger.println("ERROR: Unable to measure '" + info + "' after reconnect attempt.");
+                        m_SystemOutLogger.println("Current reader: " + m_cardManager.getTerminalName());
+                        m_SystemOutLogger.println("Current card:   " + m_cardName + " - " + m_cardManager.getATR());
+                        m_SystemOutLogger.println("ACTION REQUIRED: Re-insert the card (or power-cycle it), then press:");
+                        m_SystemOutLogger.println("  'r' to retry this algorithm   's' to skip it and continue\n");
                         Scanner sc = new Scanner(System.in);
                         String answ = sc.next();
                         m_SystemOutLogger.println(String.format("%s", answ));

AlgTest_Process/cplc.py

@@ -191,16 +191,18 @@ def get_ictype_name(icfab, ictype):
         if ictype.find('0015') != -1: return 'Philips P8WE5032'  # Philips P8WE5032, https://www.commoncriteriaportal.org/files/epfiles/2000_06.pdf
     if icfab.find('0005') != -1:
         if ictype.find('0045') != -1: return 'Infineon M7892 B11'   # https://csrc.nist.gov/csrc/media/projects/cryptographic-module-validation-program/documents/security-policies/140sp2327.pdf
-    if icfab.find('0005') != -1:
-        if ictype.find('0045') != -1: return 'Infineon M7892 B11'   # https://csrc.nist.gov/csrc/media/projects/cryptographic-module-validation-program/documents/security-policies/140sp2327.pdf
     if icfab.find('008c') != -1:
         if ictype.find('0089') != -1: return 'Tongxin THD89'   # https://www.commoncriteriaportal.org/files/epfiles/2017-28%20INF-2492.pdf
-    if icfab.find('4070') != -1:
+    if icfab.find('4070') != -1 or icfab.find('4790') != -1:
         if ictype.find('5072') != -1: return 'NXP P5CD144'   # https://csrc.nist.gov/csrc/media/projects/cryptographic-module-validation-program/documents/security-policies/140sp2774.pdf
+        if ictype.find('5167') != -1: return 'NXP P5CC081V1A'  # https://csrc.nist.gov/csrc/media/projects/cryptographic-module-validation-program/documents/security-policies/140sp2774.pdf
+        if ictype.find('5168') != -1: return 'NXP P5CD081V1A'  # https://csrc.nist.gov/csrc/media/projects/cryptographic-module-validation-program/documents/security-policies/140sp2774.pdf
     if icfab.find('5354') != -1:
         if ictype.find('0033') != -1: return 'STM ST31 ARM'  # Feitian D11CR https://docs.google.com/spreadsheets/d/10s3dA_qGvWMajv8RhCWa00x-h-1Dx6SdF9rEKN-1RIg/edit#gid=952816161
     if icfab.find('4180') != -1:
         if ictype.find('0106') != -1: return 'Atmel AT90SC25672RCT'  # https://csrc.nist.gov/CSRC/media/projects/cryptographic-module-validation-program/documents/security-policies/140sp925.pdf
+        if ictype.find('0107') != -1: return 'Atmel AT90SC12872RCFT Revision M'  # https://sec-certs.org/fips/ee14860f6bd0506d/target.pdf
+        if ictype.find('010b') != -1: return 'Atmel AT90SC28872RCU Revision G'  # https://sec-certs.org/fips/311ba2ed6a5b4105/target.pdf
     return ''
 
 

AlgTest_Process/nbproject/project.properties

@@ -32,14 +32,16 @@ dist.javadoc.dir=${dist.dir}/javadoc
 endorsed.classpath=
 excludes=
 file.reference.AlgTestJClient.jar=..\\AlgTest_JClient\\dist\\AlgTestJClient.jar
+file.reference.AlgTestJClient.jar-1=..\\libs\\AlgTestJClient.jar
 file.reference.json-simple-1.1.1.jar=..\\libs\\json-simple-1.1.1.jar
 includes=**
 jar.archive.disabled=${jnlp.enabled}
 jar.compress=false
 jar.index=${jnlp.enabled}
 javac.classpath=\
     ${file.reference.AlgTestJClient.jar}:\
-    ${file.reference.json-simple-1.1.1.jar}
+    ${file.reference.json-simple-1.1.1.jar}:\
+    ${file.reference.AlgTestJClient.jar-1}
 # Space-separated list of extra javac options
 javac.compilerargs=
 javac.deprecation=false

AlgTest_Process/run.bat

@@ -1,10 +1,10 @@
 java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles HTML
 
-java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\fixed\ SIMILARITY ..\..\algtest_results\javacard\web\
-java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\fixed\ JCINFO ..\..\algtest_results\javacard\web\
-java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\fixed\ SORTABLE ..\..\algtest_results\javacard\web\
-java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\fixed\ RADAR ..\..\algtest_results\javacard\web\
-java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\variable\ SCALABILITY ..\..\algtest_results\javacard\web\
+java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\fixed\ SIMILARITY ..\..\algtest_web\javacard\web\
+java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\fixed\ JCINFO ..\..\algtest_web\javacard\web\
+java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\fixed\ SORTABLE ..\..\algtest_web\javacard\web\
+java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\fixed\ RADAR ..\..\algtest_web\javacard\web\
+java -jar ..\AlgTest_Process\dist\AlgTestProcess.jar ..\..\algtest_results\javacard\Profiles\performance\variable\ SCALABILITY ..\..\algtest_web\javacard\web\