docs: fix deploy failure — add repository-guide to nav, remove deleted file-organisation, fix broken links

Author: hk-2029

documentation/wiki/developer-guide/internals/index.md

@@ -5,7 +5,7 @@ This section documents the internal structure of the SimPaths codebase — how i
 ## Sections
 
 - [SimPaths API](api.md) — public API reference
-- [File Organisation](file-organisation.md) — directory and package layout
+- [Repository Guide](../repository-guide.md) — directory and package layout
 - [The SimPathsModel Class](simpaths-model.md) — the central model class
 - [Start Class Implementation](start-class-implementation.md) — SimPaths-specific start class
 - [MultiRun Implementation](multirun-implementation.md) — SimPaths-specific MultiRun class

documentation/wiki/developer-guide/internals/multirun-implementation.md

@@ -30,7 +30,7 @@ To use a different config file:
 java -jar multirun.jar -config my_run.yml
 ```
 
-For configuration options, see the annotated `config/default.yml`. For the data pipeline and further reference, see [`documentation/`](documentation/README.md).
+For configuration options, see the annotated `config/default.yml`. For the data pipeline and further reference, see [`documentation/`](../../developer-guide/repository-guide.md).
 
 <!-- Projections for a workhorse model parameterised to the UK context are reported in [Bronka, P. et al. (2023). *SimPaths: an open-source microsimulation model for life course analysis* (No. CEMPA6/23), Centre for Microsimulation and Policy Analysis at the Institute for Social and Economic Research*](https://www.microsimulation.ac.uk/publications/publication-557738/), which closely reflect observed data throughout a 10-year validation window. -->
 

documentation/wiki/developer-guide/repository-guide.md

@@ -271,7 +271,7 @@ When IO is enabled, this package creates projected income paths for birth cohort
 
 CSV filenames follow the pattern `<EntityClass><RunNumber>.csv`. With a single run the suffix is `1`; with multiple runs each run produces its own numbered file.
 
-For a description of the variables in output CSV files, see `documentation/SimPaths_Variable_Codebook.xlsx`. For a description of each `reg_*`, `align_*`, and `scenario_*` input file, see [Model Parameterisation](wiki/overview/parameterisation.md) on the website.
+For a description of the variables in output CSV files, see `documentation/SimPaths_Variable_Codebook.xlsx`. For a description of each `reg_*`, `align_*`, and `scenario_*` input file, see [Model Parameterisation](../overview/parameterisation.md) on the website.
 
 ---
 
@@ -288,7 +288,7 @@ The pipeline has three independent parts: (1) initial populations, (2) regressio
 | **UKHLS** (Understanding Society) | Main household panel survey; waves 1 to O (UKDA-6614-stata) | Requires EUL licence from UK Data Service |
 | **BHPS** (British Household Panel Survey) | Historical predecessor to UKHLS; used for pre-2009 employment history | Bundled with UKHLS EUL |
 | **WAS** (Wealth and Assets Survey) | Biennial survey of household wealth; waves 1 to 7 (UKDA-7215-stata) | Requires EUL licence from UK Data Service |
-| **EUROMOD / UKMOD** | Tax-benefit microsimulation system | See [Tax-Benefit Donors (UK)](wiki/getting-started/data/tax-benefit-donors-uk.md) on the website |
+| **EUROMOD / UKMOD** | Tax-benefit microsimulation system | See [Tax-Benefit Donors (UK)](../getting-started/data/tax-benefit-donors-uk.md) on the website |
 
 ### Part 1 — Initial populations (`input/InitialPopulations/compile/`)
 

mkdocs.yml

@@ -119,6 +119,7 @@ nav:
   - Developer Guide:
       - developer-guide/index.md
       - Working in GitHub: developer-guide/working-in-github.md
+      - Repository Guide: developer-guide/repository-guide.md
       - JAS-mine Architecture:
           - developer-guide/jasmine/index.md
           - Project Structure: developer-guide/jasmine/project-structure.md
@@ -129,7 +130,6 @@ nav:
       - SimPaths Internals:
           - developer-guide/internals/index.md
           - SimPaths API: developer-guide/internals/api.md
-          - File Organisation: developer-guide/internals/file-organisation.md
           - The SimPathsModel Class: developer-guide/internals/simpaths-model.md
           - Start Class Implementation: developer-guide/internals/start-class-implementation.md
           - MultiRun Implementation: developer-guide/internals/multirun-implementation.md