[skip ci] doc: update generated wiki pages (wiki/Dataflow Graph,wiki/Search API,wiki/Engines,wiki/Analyzer,wiki/Interface,wiki/Normalized AST,wiki/Control Flow Graph,wiki/Linting and Testing,wiki/Core)

Author: actions-user

wiki/Analyzer.md

@@ -1,7 +1,7 @@
-_This document was generated from '[src/documentation/print-analyzer-wiki.ts](https://github.com/flowr-analysis/flowr/tree/main//src/documentation/print-analyzer-wiki.ts)' on 2025-10-27, 16:43:14 UTC presenting an overview of flowR's analyzer (v2.6.1, using R v4.5.0). Please do not edit this file/wiki page directly._
+_This document was generated from '[src/documentation/print-analyzer-wiki.ts](https://github.com/flowr-analysis/flowr/tree/main//src/documentation/print-analyzer-wiki.ts)' on 2025-10-28, 18:19:54 UTC presenting an overview of flowR's analyzer (v2.6.1, using R v4.5.0). Please do not edit this file/wiki page directly._
 
 We are currently working on documenting the capabilities of the analyzer (with the plugins, their loading order, etc.). In general, the code documentation
-starting with the <a href="https://github.com/flowr-analysis/flowr/tree/main//src/project/flowr-analyzer.ts#L116"><code><span title="Central class for conducting analyses with FlowR. Use the FlowrAnalyzerBuilder to create a new instance.  If you want the original pattern of creating a pipeline and running all steps, you can still do this with FlowrAnalyzer#runFull .  To inspect the context of the analyzer, use FlowrAnalyzer#inspectContext (if you are a plugin and need to modify it, use FlowrAnalyzer#context instead).">FlowrAnalyzer</span></code></a> and the <a href="https://github.com/flowr-analysis/flowr/tree/main//src/project/flowr-analyzer-builder.ts#L39"><code><span title="Builder for the FlowrAnalyzer , use it to configure all analysis aspects before creating the analyzer instance with .build() or .buildSync() .  You can add new files and folders to analyze using the constructor or the .add() method.">FlowrAnalyzerBuilder</span></code></a> 
+starting with the <a href="https://github.com/flowr-analysis/flowr/tree/main//src/project/flowr-analyzer.ts#L111"><code><span title="Central class for conducting analyses with FlowR. Use the FlowrAnalyzerBuilder to create a new instance.  If you want the original pattern of creating a pipeline and running all steps, you can still do this with FlowrAnalyzer#runFull .  To inspect the context of the analyzer, use FlowrAnalyzer#inspectContext (if you are a plugin and need to modify it, use FlowrAnalyzer#context instead).">FlowrAnalyzer</span></code></a> and the <a href="https://github.com/flowr-analysis/flowr/tree/main//src/project/flowr-analyzer-builder.ts#L39"><code><span title="Builder for the FlowrAnalyzer , use it to configure all analysis aspects before creating the analyzer instance with .build() or .buildSync() .  You can add new files and folders to analyze using the constructor or the .add() method.">FlowrAnalyzerBuilder</span></code></a> 
 should be the best starting point.
 
 - [Overview](#Overview)
@@ -61,7 +61,7 @@ In general, we work on providing a set of example repositories that demonstrate
 
 <h3 id="Plugin_Types">Plugin Types</h3>
 
-During the construction of a new <a href="https://github.com/flowr-analysis/flowr/tree/main//src/project/flowr-analyzer.ts#L116"><code><span title="Central class for conducting analyses with FlowR. Use the FlowrAnalyzerBuilder to create a new instance.  If you want the original pattern of creating a pipeline and running all steps, you can still do this with FlowrAnalyzer#runFull .  To inspect the context of the analyzer, use FlowrAnalyzer#inspectContext (if you are a plugin and need to modify it, use FlowrAnalyzer#context instead).">FlowrAnalyzer</span></code></a>, plugins of different types are applied at different stages of the analysis.
+During the construction of a new <a href="https://github.com/flowr-analysis/flowr/tree/main//src/project/flowr-analyzer.ts#L111"><code><span title="Central class for conducting analyses with FlowR. Use the FlowrAnalyzerBuilder to create a new instance.  If you want the original pattern of creating a pipeline and running all steps, you can still do this with FlowrAnalyzer#runFull .  To inspect the context of the analyzer, use FlowrAnalyzer#inspectContext (if you are a plugin and need to modify it, use FlowrAnalyzer#context instead).">FlowrAnalyzer</span></code></a>, plugins of different types are applied at different stages of the analysis.
 These plugins are grouped by their <a href="https://github.com/flowr-analysis/flowr/tree/main//src/project/plugins/flowr-analyzer-plugin.ts#L28"><code><span title="Based on *when* and *what-for* the plugin is applied during the analysis, plugins are categorized into different types.  Consult this diagram for an overview of orders and (implicit or explicit) dependencies:    ┌───────────┐ ┌───────────────────┐ ┌─────────────┐ ┌───────────────┐ ┌───────┐ │ │ │ │ │ │ │ │ │ │ │ *Builder* ├──▶│ Project Discovery ├──▶│ File Loader ├──▶│ Dependencies ├──▶│ *DFA* │ │...">PluginType</span></code></a> and are applied in the following order (as shown in the documentation of the <a href="https://github.com/flowr-analysis/flowr/tree/main//src/project/plugins/flowr-analyzer-plugin.ts#L28"><code><span title="Based on *when* and *what-for* the plugin is applied during the analysis, plugins are categorized into different types.  Consult this diagram for an overview of orders and (implicit or explicit) dependencies:    ┌───────────┐ ┌───────────────────┐ ┌─────────────┐ ┌───────────────┐ ┌───────┐ │ │ │ │ │ │ │ │ │ │ │ *Builder* ├──▶│ Project Discovery ├──▶│ File Loader ├──▶│ Dependencies ├──▶│ *DFA* │ │...">PluginType</span></code></a>):
 
 ```text