The Analysis window is used to repair all the links to disambiguation pages on the opened article. You reach this window by clicking on the Full analysis button of the main window. This window looks like this:
The Tools menu is used to fix redirect links and view the page with the templates' code included.
The Options menu is used to select what type of pages are shown in the list and what type are counted.
The Sort menu is used to choose how the list of links is sorted. Sort orders can be configured to suit your needs. (See Sorting options).
The Close after sending checkbox specifies if the window will be automatically closed after sending the page to Wikipedia.
The Add a note on talk page checkbox specifies if you want to post a comment on the talk page of the article after sending the page to Wikipedia.
The Update disambiguation warning on talk page[1] checkbox specifies if you want to update the disambiguation warning on talk page if it's already there.
The Create disambiguation warning on talk page[1] checkbox specifies if you want to add the disambiguation warning on talk page if there are still links to disambiguation pages.
The Automatic comment checkbox specifies if you want to use the default comment when updating the page on Wikipedia.
On the right part of the window, there is the text of the current page and a set of buttons:
You can right click in the text on an internal link [[...]], a template {{...}} or an external link [http://...] to bring up a contextual menu that has useful features.
The , , and buttons find other occurrences of the links you have selected in the list.
The and buttons undo or redo a modification you have made.
The button lets you see and edit the table of contents of the article.
The [1] button activates some spelling and typography checks.
The [1] buttons lets you add categories for a redirect page.
The button validates your modifications. It updates the count of links found for each disambiguation page in the left list, updates the main display, and memorizes the new text (for Undo/Redo).
The button updates the page on Wikipedia. It is unavailable until a modification has been made on the page.
The button deletes the page on Wikipedia.[2]
The [1] button updates the disambiguation warning on the talk page.
The button reloads the page from Wikipedia (your current modifications will be lost).
The [3] button opens the current page in your web browser.
The [3] button opens the current page history in your web browser.
The button opens a new window to analyze the page as a disambiguation page.
The (??) ⇒ (en) button helps translating an article coming from an other language, by translating internal links, templates and categories.
The time of the last modification of the page is displayed (in orange or in red if modifications are recent).
If the page is protected, the protection level is displayed.
On the left part of the window, there is a list of links found in the page:
In the above example, you can see that the page Antalla contains links to 2 disambiguation pages (Algheden and Barentu), followed by the number of occurrences (in this case, one each). You can right click on any item in the list to bring a contextual menu with useful features.
Above the list are the button, which allows you to analyze the selected page(s) in the list, the button which allows you to analyze the selected page(s) as a disambiguation page, and the Add to watch list button which allows you to add the selected page(s) to your local watchlist.
Below, the list of links, there is a list of errors detected by the Check Wikipedia[1] project.
By selecting a page (or several) in the left list, the matching links are highlighted in the text (in bold, with either red, orange, or blue), and the display is shifted (if necessary) to show the first link found. Dealing with the individual situations is described below.
Dealing with links displayed in red
By selecting a page in the left list, some matching links are highlighted in the text in bold and in red. This is used when WPCleaner thinks that the links need to be repaired. By clicking with the right button of your mouse, a contextual menu is displayed, letting you do semi-automatic modifications.
The available options in this menu are:
Link to: Move the link to another page, but keep the displayed text. Links to wiktionary pages[1] are also available when necessary.
Replace with: Move the link to another page, and change the displayed text.
Add to preferred disambiguations: Add a link to the list of preferred links to solve this disambiguation. Preferred links appears first in the Link to and Replace with options.
Reverse to ...: Swap the link and the text ([[xx|yy]] becomes [[yy|xx]]).
Remove link: Remove the link to the disambiguation page, keeping only the displayed text.
Mark as normal link[1]: Mark the link as being correct.
Analyze: Analyze the page of the selected link. This allows you to study the content of the page before repairing the link.
External Viewer[3]: Display the page of the selected link in your web browser.
History[3]: Display the history of the selected link in your web browser.
Disambiguation analysis: Analyze the page of the selected link as a disambiguation page.
Reload links: Reload the list of links.
In the Antalla example, the repairing can be done this way:
When the page is initially displayed, Algheden and Barentu are automatically selected in the left list and highlighted in the text.
By right-clicking on the [[Barentu]] link, the contextual menu is displayed. By highlighting Link to, we can see the available pages to link to. In this case, Barentu, Eritrea is the correct page. You may fix the link by selecting Link to → Barentu, Eritrea in the menu.
Click on to validate the modification. The number of links found is updated in the left list. The link to Algheden stays highlighted in the text.
By right clicking on the [[Algheden]] link, the contextual menu is displayed. The repairing is not obvious in this situation; we don't know what is the correct link. Ask for help by choosing Mark as needing help.
Click on to be sure that all links have been repaired.
By selecting a page in the left list, some matching links are highlighted in the text in both bold and orange. This is when the link is either to a redirect page, is broken, or has been marked as needing help. Broken links are signified with a strikethrough. Redirect links can be bypassed either by right-clicking the link in the page text and choosing an option, or clicking on Tools menu on the top left of the window, and selecting the specific page. Links for which help is requested can be dealt with like links displayed in red.
Please note that there are many instances where links to redirect pages or red links should not be 'repaired'.
For guidance, please see the appropriate sections in WP:Redirect or WP:RED.
Dealing with links displayed in blue
By selecting a page in the left list, some matching links are highlighted in the text in both bold and blue. This is when WPCleaner thinks that the link does not need to be repaired, either because it has been previously identified as correctly directing to a disambiguation page, or is just a normal link.
Special situations
In some situations, WPCleaner doesn't find the links to disambiguation pages in the page text. This could be for multiple reasons:
The link is in a template used in the page. In this situation, it's the template that needs to be repaired to remove the disambiguation link from the page.
A special situation. If you believe that this situation can happen quite frequently, you can tell me so that I add this situation.
Several features are available to help in these situations:
Finding a word in the text: either by using Ctrl+F in the text of the page, or by right clicking on the left list (Option Find text in the contextual menu).
Analyzing templates used in the page: by right clicking on the left list (Option Analyze templates in the contextual menu). This feature displays a separate window listing all the templates in the page that have links to the selected disambiguation page. By double clicking on the template name, a window is displayed to repair the links in the model.
Notes
^ a b c d e f g h iThis feature may not be available for every Wikipedia. Such features can be added by configuring WPCleaner for the desired Wikipedia
^This button is only available for users with the right to delete pages
^ a b c dTo use this feature, you need Java release 6 or more.
WPCleaner – 2.05 (August 26, 2022) [±]
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buttons find other occurrences of the links you have selected in the list.
and 
buttons undo or redo a modification you have made.
button lets you see and edit the table of contents of the article.
[1] button activates some spelling and typography checks.
[1] buttons lets you add categories for a redirect page.
button validates your modifications. It updates the count of links found for each disambiguation page in the left list, updates the main display, and memorizes the new text (for Undo/Redo).
button updates the page on Wikipedia. It is unavailable until a modification has been made on the page.
button deletes the page on Wikipedia.[2]
[1] button updates the disambiguation warning on the talk page.
button reloads the page from Wikipedia (your current modifications will be lost).
[3] button opens the current page in your web browser.
[3] button opens the current page history in your web browser.
button opens a new window to analyze the page as a disambiguation page.
button, which allows you to analyze the selected page(s) in the list, the 
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