The -U (Undefined) preprocessor symbols are deleted

[psuzzi]

Describe the bug
In My CDT C Project, from Project Properties > C/C++Build > Settings, in the Tool Settings tab under the node Cross GCC Compiler > Preprocessor - I can set Undefined Symbols correctly. (see image-1)
But when I go to Project Properties > C/C++ General > Paths and Symbols, in the Symbols tab - to set Preprocessor Symbols, after applying, the Undefined Symbols set previously are removed

To Reproduce
Steps to reproduce the behavior:

• Go to "C/C++ Build > Settings > Tool Settings > C Compiler > Preprocessor"
• Add undefined symbols in "Undefined symbols (-U)" section (e.g., UNDEF1, UNDEF2)
• Apply and close
• Go to "C/C++ General > Paths and Symbols > Symbols"
• Add any new defined symbol (e.g., TEST_SYMBOL=1)
• Apply and close
• Return to "C/C++ Build > Settings" - undefined symbols are gone

Expected behavior
The undefined symbols are not deleted from the C Compiler > Preprocessor

Screenshots
These screenshots guide to reproduce the bug:

Version Information (please complete the following information):

• OS and OS Version/extra details: Windows 10
• Eclipse Version from Help -> About Version: 2024-12 (4.34.0)
• CDT Version from Help -> About -> Installation Details -> Features tab : Eclipse CDT C/C++ Development Platform 11.2.0.202306051917 org.eclipse.cdt.platform

Additional context
To identify the issue, just set a breakpoint in ResourceInfo.setOption(IHoldsOptions, IOption, String[])
And observe that every time we call the CLanguageSetting.setSettingEntries(int, List), de facto we read all the preprocessor symbols and rewrite them, except for the Undefined options.

[psuzzi]

Additional Details:

This is the stacktrace:

FolderInfo(ResourceInfo).setOption(IHoldsOptions, IOption, String[]) line: 362	
ManagedBuildManager.setOption(IResourceInfo, IHoldsOptions, IOption, String[]) line: 1035	
BuildEntryStorage.setUserUndefinedStringSet(Set<String>) line: 793	
BuildEntryStorage.obtainEntriesFromLevel(int, SettingsSet$SettingLevel) line: 155	
BuildEntryStorage(AbstractEntryStorage).setEntries(ICLanguageSettingEntry[]) line: 66	
BuildLanguageData.setEntries(int, ICLanguageSettingEntry[]) line: 106	
CLanguageSetting.setSettingEntries(int, CLanguageData, EntryStore) line: 339	
CLanguageSetting.setSettingEntries(int, List<ICLanguageSettingEntry>) line: 327	
...

A good idea for solving would be considering to preserve also the Undefined options, looking for them among the IOptions.

Call stack details below, from setSettingEntries:

CLanguageSetting.setSettingEntries(int, List) - CDT code

	@Override
	public void setSettingEntries(int kind, List<ICLanguageSettingEntry> list) {
		CLanguageData data = getCLanguageData(true);
		EntryStore store = new EntryStore();
		//		KindBasedStore nameSetStore = new KindBasedStore();
		int eKind;

		if (list != null) {
			if (list.size() != 0) {
				for (ICLanguageSettingEntry entry : list) {
					eKind = entry.getKind();
					if ((kind & eKind) != 0 && (data.getSupportedEntryKinds() & eKind) != 0) {
						store.addEntry(entry);
					}
				}
			} else {
				int kinds[] = KindBasedStore.getLanguageEntryKinds();
				for (int k : kinds) {
					if ((k & kind) != 0) {
						store.storeEntries(k, new ICLanguageSettingEntry[0]);
					}
				}
			}
		}

		setSettingEntries(kind, data, store); // STACK CALL HERE
	}

then it calls CLanguageSetting.setSettingEntries(int, CLanguageData, EntryStore) line: 339 - CDT code

	private void setSettingEntries(int kind, CLanguageData data, EntryStore store) {
		int oredk = getSupportedEntryKinds();
		int kinds[] = flagsToArray(oredk);

		//		int kinds[] = KindBasedStore.getSupportedKinds();
		for (int i = 0; i < kinds.length; i++) {
			ICLanguageSettingEntry sortedEntries[] = store.containsEntriesList(kinds[i]) ? store.getEntries(kinds[i])
					: null;
			if ((kind & kinds[i]) != 0) {
				data.setEntries(kinds[i], sortedEntries); // STACK CALL HERE
				if (sortedEntries == null)
					CExternalSettingsManager.getInstance().restoreDefaults(this, kind);
			}
		}
	}

thern calls BuildLanguageData.setEntries(int, ICLanguageSettingEntry[]) line: 106 - CDT code

	@Override
	public void setEntries(int kind, ICLanguageSettingEntry entries[]) {
		BuildEntryStorage storage = getEntryStorage(kind);
		if (storage != null)
			storage.setEntries(entries); // STACK CALL HERE
	}

then calls BuildEntryStorage(AbstractEntryStorage).setEntries(ICLanguageSettingEntry[]) line: 66 - CDT code

	public void setEntries(ICLanguageSettingEntry entries[]) {
		if (entries == null) {
			resetDefaults();
			return;
		}
		SettingsSet settings = initCache();

		settings.applyEntries(entries);

		SettingLevel levels[] = settings.getLevels();

		for (int i = 0; i < levels.length; i++) {
			obtainEntriesFromLevel(i, levels[i]); // STACK CALL HERE
		}
	}

Then calls BuildEntryStorage.obtainEntriesFromLevel(int, SettingsSet$SettingLevel) line: 155 - CDT code

	@Override
	protected void obtainEntriesFromLevel(int levelNum, SettingLevel level) {
		switch (levelNum) {
		case USER_ENTRIES_LEVEL:
			if (level == null) {
				restoreDefaults();
			} else {
				EntryInfo infos[] = level.getInfos();
				UserEntryInfo[] userInfos = new UserEntryInfo[infos.length];
				for (int i = 0; i < infos.length; i++) {
					UserEntryInfo uei = (UserEntryInfo) infos[i].getCustomInfo();
					if (uei == null)
						uei = new UserEntryInfo(infos[i].getEntry(), null, null, null);
					userInfos[i] = uei;
				}
				@SuppressWarnings("unchecked")
				List<EmptyEntryInfo> context = (List<EmptyEntryInfo>) level.getContext();
				setUserEntries(userInfos, context);
				setUserUndefinedStringSet(level.containsOverrideInfo() ? level.getOverrideSet() : null); // STACK CALL HERE
			}
			break;
		}
	}

then calls BuildEntryStorage.setUserUndefinedStringSet(Set) line: 793 - CDT code

	private void setUserUndefinedStringSet(Set<String> set) {
		int kind = getKind();
		IOption[] options = fLangData.getUndefOptionsForKind(kind);
		if (options.length != 0) {
			if (set != null && set.size() == 0)
				set = null;

			String[] optValue = set != null ? (String[]) set.toArray(new String[set.size()]) : new String[0];
			IOption option = options[0];
			ITool tool = fLangData.getTool();
			IResourceInfo rcInfo = tool.getParentResourceInfo();
			IOption newOption = ManagedBuildManager.setOption(rcInfo, tool, option, optValue); // STACK CALL HERE
			options = fLangData.getUndefOptionsForKind(kind);
			for (IOption opt : options) {
				if (opt != newOption)
					ManagedBuildManager.setOption(rcInfo, tool, option, new String[0]);
			}
		}
	}

then calls ManagedBuildManager.setOption(IResourceInfo, IHoldsOptions, IOption, String[]) line: 1035 - CDT code

	/**
	 * Set the string array value for an option for a given resource config.
	 *
	 * @param resConfig The resource configuration the option belongs to.
	 * @param holder The holder/parent of the option.
	 * @param option The option to set the value for.
	 * @param value The values the option should contain after the change.
	 *
	 * @return The modified option.  This can be the same option or a newly created option.
	 *
	 * @since 3.0 - The type and name of the <code>ITool tool</code> parameter
	 *        has changed to <code>IHoldsOptions holder</code>. Client code
	 *        assuming <code>ITool</code> as type, will continue to work unchanged.
	 */
	public static IOption setOption(IResourceInfo resConfig, IHoldsOptions holder, IOption option, String[] value) {
		IOption retOpt;
		try {
			retOpt = resConfig.setOption(holder, option, value); // STACK CALL HERE
			if (retOpt.getValueHandler().handleValue(resConfig, holder, retOpt, retOpt.getValueHandlerExtraArgument(),
					IManagedOptionValueHandler.EVENT_APPLY)) {
				// TODO : Event is handled successfully and returned true.
				// May need to do something here say log a message.
			} else {
				// Event handling Failed.
			}
		} catch (BuildException e) {
			return null;
		}
		return retOpt;
	}

which finally calls FolderInfo(ResourceInfo).setOption(IHoldsOptions, IOption, String[]) line: 362 - CDT code

	@Override
	public IOption setOption(IHoldsOptions parent, IOption option, String[] value) throws BuildException {
		IOption retOpt = option;
		// Is there a change?
		String[] oldValue;
		switch (option.getBasicValueType()) {
		case IOption.STRING_LIST:
			oldValue = option.getBasicStringListValue();
			break;
		default:
			oldValue = new String[0];
			break;
		}
		if (!Arrays.equals(value, oldValue)) {
			retOpt = parent.getOptionToSet(option, false);
			retOpt.setValue(value);
			propagate(parent, option, oldValue, value);
			NotificationManager.getInstance().optionChanged(this, parent, option, oldValue);
		}
		return retOpt;
	}